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From: Colin <col...@gm...> - 2018-11-05 14:10:52
|
You're welcome! I am cc'ing the gmo...@li... list email here for posterity (wrong email for the list was here previously) -Colin On Mon, Nov 5, 2018 at 8:55 AM Seyed Ahmad Mousavi <ahm...@gm...> wrote: > Thanks Colin for complete answer. > > On Mon, Nov 5, 2018 at 5:24 PM Colin D <col...@gm...> wrote: > >> The mod_deflate is an option of the webserver e.g. Apache rather than >> JBrowse. You can maybe run the command for apache 2 >> >> >> >> sudo a2enmod deflate >> >> >> >> This enables the mod_deflate module >> >> Then I added to my apache2.conf file “AddOutputFilterByType DEFLATE >> text/html text/plain text/xml text/css application/json” where >> application/json applies to the refSeqs.json >> >> >> >> I can then test that it was applied correctly by getting >> Content-Encoding: gzip on json files >> >> >> >> % curl -I -H 'Accept-Encoding: gzip,deflate' >> http://localhost/jbrowse/sample_data/json/volvox/seq/refSeqs.json >> >> HTTP/1.1 200 OK >> >> Date: Mon, 05 Nov 2018 13:51:39 GMT >> >> Server: Apache/2.4.18 (Ubuntu) >> >> Last-Modified: Sat, 03 Nov 2018 16:12:58 GMT >> >> ETag: "93-579c4eceb4d7b-gzip" >> >> Accept-Ranges: bytes >> >> Vary: Accept-Encoding >> >> Content-Encoding: gzip >> >> Content-Length: 101 >> >> Content-Type: application/json >> >> >> >> >> >> -Colin >> >> >> ------------------------------ >> *From:* Seyed Ahmad Mousavi <ahm...@gm...> >> *Sent:* Monday, November 5, 2018 8:34:44 AM >> *To:* Colin >> *Cc:* gmo...@so... >> *Subject:* Re: Slow loading Jbrowse >> >> Dear Colin, >> >> Thanks for fast reply. >> >> Yes, my genome is really sparse about 150K sequence fragment. >> >> Sorry could you explain more about where exactly should I apply *mod_deflate >> *option ?? >> >> Best wishes, >> Ahmad >> >> On Mon, Nov 5, 2018 at 5:01 PM Colin <col...@gm...> wrote: >> >>> Hi Seyed, >>> The most common cause of a slow startup time would be having a very >>> fragmented genome because jbrowse loads the list of the names of the >>> contigs at startup e.g. the refSeqs.json file. This sometimes results in >>> download tens of megabytes of data before anything else loads. If possible >>> you might apply a cutoff for your sequence length. Alternatively you can >>> apply gzip compression server side e.g. with mod_deflate which will just >>> save time in downloading the initial list of sequences. >>> >>> -Colin >>> >>> On Mon, Nov 5, 2018, 7:37 AM Seyed Ahmad Mousavi < >>> ahm...@gm... wrote: >>> >>>> Hello >>>> >>>> I have used JBrowse for my project, which is a new genome, I have added >>>> several tracks to it. (genome size = 1.5G with 7 gtf tracks) >>>> >>>> But the start time of Jbrowse website takes too long, for e.g. its >>>> takes 3-4 mins every time I wanted to see the website which is too much. >>>> >>>> Is it normal to takes 3 mins every time? >>>> >>>> How can I solve this problem? >>>> >>>> >>>> Thanks, >>>> Ahmad >>>> >>> |
|
From: Garrett S. <ste...@gm...> - 2018-10-26 13:12:14
|
I see where you found that link in the documentation. It's not correct, sorry about that. I'll try to get it fixed soon. To download the newest desktop version you can go to http://jbrowse.org/blog/ and download the file called JBrowse-1.15.4-desktop-linux-x64.zip (or the corresponding one if you're not using linux). Unzip it and launch the file JBrowse-1.15.4-desktop. If it doesn't work, you may need to install libgconf, which can be installed on some linux systems by running sudo apt install libgconf-2-4 Let us know if you still have problems. ~Garrett On Fri, Oct 26, 2018 at 3:28 AM Beatrice Kodero <kod...@gm...> wrote: > Thanks, I am tying to open it in http://jbrowse.org/jbrowse-1-12-1/ but > getting an error message. > > On Wed, Oct 24, 2018 at 10:02 PM Garrett Stevens < > ste...@gm...> wrote: > >> The desktop version should be able to open VCF files. I was just able to >> open one on my computer. If you let us know what you have tried and what >> error you got, maybe we can help. >> >> ~Garrett >> >> On Wed, Oct 24, 2018 at 2:56 PM Beatrice Kodero <kod...@gm...> >> wrote: >> >>> Thanks for your continued support. I heartily appreciate. >>> >>> Desktop was my choice but could not load VCF files >>> >>> On Wed, Oct 24, 2018 at 5:09 PM Garrett Stevens < >>> ste...@gm...> wrote: >>> >>>> The general idea is to put the data you want to visualize in the data >>>> directory (probably /var/www/html/jbrowse/data for you) and then add >>>> track entries that reference that data to either tracks.conf or >>>> trackList.json in the data directory. Either the conf or json files >>>> work, they can do the same things. >>>> >>>> For reference, the configuration files for that site you linked can be >>>> viewed at http://jbrowse.igs.umaryland.edu/t_parva/data/trackList.json >>>> and http://jbrowse.igs.umaryland.edu/t_parva/data/tracks.conf. There >>>> are lots of different types of tracks, so to configure the specific types >>>> of tracks you want you'll have to look at our documentation >>>> <http://jbrowse.org/docs/reference_sequence.html> under "Configuring >>>> Tracks." >>>> >>>> Another option if you're only viewing locally is JBrowse Desktop >>>> <http://jbrowse.org/docs/jbrowse_desktop.html>, which can load your >>>> data and then save your session so you can come back to the same data later. >>>> >>>> ~Garrett >>>> >>>> On Tue, Oct 23, 2018 at 8:49 PM Beatrice Kodero <kod...@gm...> >>>> wrote: >>>> >>>>> I am new to Linux and this is my first system to install. >>>>> >>>>> Would like to customise , have day preloaded ( like link sent before) >>>>> and visualize data locally of T.parva genomes >>>>> >>>>> Apologies for to many questions ;-) >>>>> >>>>> On Wed, Oct 24, 2018, 2:44 AM Beatrice Kodero <kod...@gm...> >>>>> wrote: >>>>> >>>>>> >>>>>> Please allow me to ask, After installation and I want to preload data >>>>>> to my localhost ie i don't have to upload a reference gene or add track >>>>>> something like this here >>>>>> >>>>>> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >>>>>> What files will i work with? jbrowse.conf or tracks.conf or hard code? >>>>>> >>>>>> Regards >>>>>> Beatrice >>>>>> >>>>>> On Tue, Oct 23, 2018, 9:40 PM Beatrice Kodero <kod...@gm...> >>>>>> wrote: >>>>>> >>>>>>> Hey Scott, >>>>>>> >>>>>>> It's blank >>>>>>> >>>>>>> On Tue, Oct 23, 2018, 9:06 PM Scott Cain <sc...@sc...> >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Beatrice, >>>>>>>> >>>>>>>> I can’t quite make out the text in the red bar (where the error >>>>>>>> message is). Can you tell us what it says? >>>>>>>> >>>>>>>> Thanks, Scott >>>>>>>> >>>>>>>> On Oct 23, 2018, at 10:31 AM, Beatrice Kodero <kod...@gm...> >>>>>>>> wrote: >>>>>>>> >>>>>>>> Please find attached. The error I am now getting from installation >>>>>>>> >>>>>>>> On Tue, Oct 23, 2018 at 8:21 PM Beatrice Kodero < >>>>>>>> kod...@gm...> wrote: >>>>>>>> >>>>>>>>> Garrett Thanks a million. >>>>>>>>> >>>>>>>>> Able to download at cd/var/www/html/jbrowse >>>>>>>>> >>>>>>>>> Please allow me to ask, After installation and I want to preload >>>>>>>>> data to my localhost ie i don't have to upload a reference gene or add >>>>>>>>> track something like this here >>>>>>>>> >>>>>>>>> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >>>>>>>>> What files will i work with? jbrowse.conf or tracks.conf or hard >>>>>>>>> code. >>>>>>>>> >>>>>>>>> On Tue, Oct 23, 2018 at 7:47 PM Garrett Stevens < >>>>>>>>> ste...@gm...> wrote: >>>>>>>>> >>>>>>>>>> Either should work, as long as you specify the paths to the files >>>>>>>>>> correctly. E.g. >>>>>>>>>> >>>>>>>>>> cd /var/www/html/jbrowse >>>>>>>>>> bgzip data/volvox.sorted.gff3 tabix -p gff >>>>>>>>>> data/volvox.sorted.gff3.gz >>>>>>>>>> >>>>>>>>>> and >>>>>>>>>> >>>>>>>>>> cd /var/www/html/jbrowse/data >>>>>>>>>> bgzip volvox.sorted.gff3 tabix -p gff volvox.sorted.gff3.gz >>>>>>>>>> >>>>>>>>>> should both work. >>>>>>>>>> >>>>>>>>>> ~Garrett >>>>>>>>>> >>>>>>>>>> On Tue, Oct 23, 2018 at 12:00 PM Beatrice Kodero < >>>>>>>>>> kod...@gm...> wrote: >>>>>>>>>> >>>>>>>>>>> thanks for your mail again, >>>>>>>>>>> >>>>>>>>>>> kindly clarify should I be /var/www/html/jbrowse/data or >>>>>>>>>>> /var/www/html/jbrowse >>>>>>>>>>> >>>>>>>>>>> Been working from /var/www/html/jbrowse/data to install content >>>>>>>>>>> of https://jbrowse.org/docs/tutorial.html ie FASTA, GFF3 >>>>>>>>>>> >>>>>>>>>>> Thanks >>>>>>>>>>> >>>>>>>>>>> On Tue, Oct 23, 2018 at 6:50 PM Garrett Stevens < >>>>>>>>>>> ste...@gm...> wrote: >>>>>>>>>>> >>>>>>>>>>>> Ok, so looking at the error in your first message, it looks >>>>>>>>>>>> like you perhaps weren't in the right location when you ran the bgzip and >>>>>>>>>>>> tabix commands. Those are the commands that will generate the files you are >>>>>>>>>>>> missing. Try making sure you cd to the right directory first, >>>>>>>>>>>> like: >>>>>>>>>>>> >>>>>>>>>>>> cd /var/www/html/jbrowse >>>>>>>>>>>> bgzip data/volvox.sorted.gff3 tabix -p gff >>>>>>>>>>>> data/volvox.sorted.gff3.gz >>>>>>>>>>>> >>>>>>>>>>>> ~Garrett >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero < >>>>>>>>>>>> kod...@gm...> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Thanks for apt response Garrett >>>>>>>>>>>>> >>>>>>>>>>>>> I am following step step process on the link http://jbrowse.org/docs/installation.html >>>>>>>>>>>>> . >>>>>>>>>>>>> >>>>>>>>>>>>> <http://jbrowse.org/docs/installation.html> >>>>>>>>>>>>> I used wget and downloaded above. The challenge am facing >>>>>>>>>>>>> begins at http://jbrowse.org/docs/tutorial.html >>>>>>>>>>>>> >>>>>>>>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa >>>>>>>>>>>>> >>>>>>>>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 >>>>>>>>>>>>> >>>>>>>>>>>>> I only got these files >>>>>>>>>>>>> tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 >>>>>>>>>>>>> >>>>>>>>>>>>> Instead of below files >>>>>>>>>>>>> /var/www/html/jbrowse >>>>>>>>>>>>> /var/www/html/jbrowse/data >>>>>>>>>>>>> /var/www/html/jbrowse/data/volvox.fa >>>>>>>>>>>>> /var/www/html/jbrowse/data/volvox.fa.fai >>>>>>>>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz >>>>>>>>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi >>>>>>>>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam >>>>>>>>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam.bai >>>>>>>>>>>>> /var/www/html/jbrowse/data/tracks.conf >>>>>>>>>>>>> >>>>>>>>>>>>> I am missing >>>>>>>>>>>>> >>>>>>>>>>>>> volvox.sorted.gff3.gz >>>>>>>>>>>>> >>>>>>>>>>>>> volvox.sorted.gff3.gz.tbi >>>>>>>>>>>>> >>>>>>>>>>>>> Kindly advise. >>>>>>>>>>>>> >>>>>>>>>>>>> Regards >>>>>>>>>>>>> >>>>>>>>>>>>> Beatrice >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens < >>>>>>>>>>>>> ste...@gm...> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hello, >>>>>>>>>>>>>> >>>>>>>>>>>>>> When you say the curl link is not working, what do you mean? >>>>>>>>>>>>>> Are you using the installation instructions found here >>>>>>>>>>>>>> <http://jbrowse.org/docs/installation.html>? I tried the >>>>>>>>>>>>>> curl command on that page and it worked fine for me: >>>>>>>>>>>>>> >>>>>>>>>>>>>> curl -O >>>>>>>>>>>>>> https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >>>>>>>>>>>>>> >>>>>>>>>>>>>> Also the output you pasted was something with bgzip, not >>>>>>>>>>>>>> curl, so I'm not sure what the problem is there. If you can give some more >>>>>>>>>>>>>> detail we can see if we can help. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>> Garrett >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero < >>>>>>>>>>>>>> kod...@gm...> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi , >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> I trust that this email finds you well. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> I am at the point of installing jbowse and the curl link is >>>>>>>>>>>>>>> not working. see below installation >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> bgzip data/volvox.sorted.gff3 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [bgzip] No such file or directory: >>>>>>>>>>>>>>> data/volvox.sorted.gff3...........error am getting. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> What could i be doing wrong? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Regards, >>>>>>>>>>>>>>> Beatrice Kodero >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> "Winning means you're willing to go longer, work harder, and >>>>>>>>>>>>>>> give more than anyone else." Vince Lombardi >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>>>>>>>> Skype : B.Kodero >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> Gmod-ajax mailing list >>>>>>>>>>>>>>> Gmo...@li... >>>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> >>>>>>>>>>>>> Regards, >>>>>>>>>>>>> Beatrice Kodero >>>>>>>>>>>>> >>>>>>>>>>>>> "Winning means you're willing to go longer, work harder, and >>>>>>>>>>>>> give more than anyone else." Vince Lombardi >>>>>>>>>>>>> >>>>>>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>>>>>> Skype : B.Kodero >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> Regards, >>>>>>>>>>> Beatrice Kodero >>>>>>>>>>> >>>>>>>>>>> "Winning means you're willing to go longer, work harder, and >>>>>>>>>>> give more than anyone else." Vince Lombardi >>>>>>>>>>> >>>>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>>>> Skype : B.Kodero >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> Regards, >>>>>>>>> Beatrice Kodero >>>>>>>>> >>>>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>>>> more than anyone else." Vince Lombardi >>>>>>>>> >>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>> Skype : B.Kodero >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> Regards, >>>>>>>> Beatrice Kodero >>>>>>>> >>>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>>> more than anyone else." Vince Lombardi >>>>>>>> >>>>>>>> Mobile : +254 726 486 077 >>>>>>>> Skype : B.Kodero >>>>>>>> >>>>>>>> <WhatsApp Image 2018-10-23 at 8.28.07 PM(1).jpeg> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Gmod-ajax mailing list >>>>>>>> Gmo...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>>>> >>>>>>>> >>> >>> -- >>> >>> Regards, >>> Beatrice Kodero >>> >>> "Winning means you're willing to go longer, work harder, and give more >>> than anyone else." Vince Lombardi >>> >>> Mobile : +254 726 486 077 >>> Skype : B.Kodero >>> >> > > -- > > Regards, > Beatrice Kodero > > "Winning means you're willing to go longer, work harder, and give more > than anyone else." Vince Lombardi > > Mobile : +254 726 486 077 > Skype : B.Kodero > |
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From: Beatrice K. <kod...@gm...> - 2018-10-26 07:28:30
|
Thanks, I am tying to open it in http://jbrowse.org/jbrowse-1-12-1/ but getting an error message. On Wed, Oct 24, 2018 at 10:02 PM Garrett Stevens < ste...@gm...> wrote: > The desktop version should be able to open VCF files. I was just able to > open one on my computer. If you let us know what you have tried and what > error you got, maybe we can help. > > ~Garrett > > On Wed, Oct 24, 2018 at 2:56 PM Beatrice Kodero <kod...@gm...> > wrote: > >> Thanks for your continued support. I heartily appreciate. >> >> Desktop was my choice but could not load VCF files >> >> On Wed, Oct 24, 2018 at 5:09 PM Garrett Stevens < >> ste...@gm...> wrote: >> >>> The general idea is to put the data you want to visualize in the data >>> directory (probably /var/www/html/jbrowse/data for you) and then add >>> track entries that reference that data to either tracks.conf or >>> trackList.json in the data directory. Either the conf or json files >>> work, they can do the same things. >>> >>> For reference, the configuration files for that site you linked can be >>> viewed at http://jbrowse.igs.umaryland.edu/t_parva/data/trackList.json >>> and http://jbrowse.igs.umaryland.edu/t_parva/data/tracks.conf. There >>> are lots of different types of tracks, so to configure the specific types >>> of tracks you want you'll have to look at our documentation >>> <http://jbrowse.org/docs/reference_sequence.html> under "Configuring >>> Tracks." >>> >>> Another option if you're only viewing locally is JBrowse Desktop >>> <http://jbrowse.org/docs/jbrowse_desktop.html>, which can load your >>> data and then save your session so you can come back to the same data later. >>> >>> ~Garrett >>> >>> On Tue, Oct 23, 2018 at 8:49 PM Beatrice Kodero <kod...@gm...> >>> wrote: >>> >>>> I am new to Linux and this is my first system to install. >>>> >>>> Would like to customise , have day preloaded ( like link sent before) >>>> and visualize data locally of T.parva genomes >>>> >>>> Apologies for to many questions ;-) >>>> >>>> On Wed, Oct 24, 2018, 2:44 AM Beatrice Kodero <kod...@gm...> >>>> wrote: >>>> >>>>> >>>>> Please allow me to ask, After installation and I want to preload data >>>>> to my localhost ie i don't have to upload a reference gene or add track >>>>> something like this here >>>>> >>>>> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >>>>> What files will i work with? jbrowse.conf or tracks.conf or hard code? >>>>> >>>>> Regards >>>>> Beatrice >>>>> >>>>> On Tue, Oct 23, 2018, 9:40 PM Beatrice Kodero <kod...@gm...> >>>>> wrote: >>>>> >>>>>> Hey Scott, >>>>>> >>>>>> It's blank >>>>>> >>>>>> On Tue, Oct 23, 2018, 9:06 PM Scott Cain <sc...@sc...> wrote: >>>>>> >>>>>>> Hi Beatrice, >>>>>>> >>>>>>> I can’t quite make out the text in the red bar (where the error >>>>>>> message is). Can you tell us what it says? >>>>>>> >>>>>>> Thanks, Scott >>>>>>> >>>>>>> On Oct 23, 2018, at 10:31 AM, Beatrice Kodero <kod...@gm...> >>>>>>> wrote: >>>>>>> >>>>>>> Please find attached. The error I am now getting from installation >>>>>>> >>>>>>> On Tue, Oct 23, 2018 at 8:21 PM Beatrice Kodero <kod...@gm...> >>>>>>> wrote: >>>>>>> >>>>>>>> Garrett Thanks a million. >>>>>>>> >>>>>>>> Able to download at cd/var/www/html/jbrowse >>>>>>>> >>>>>>>> Please allow me to ask, After installation and I want to preload >>>>>>>> data to my localhost ie i don't have to upload a reference gene or add >>>>>>>> track something like this here >>>>>>>> >>>>>>>> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >>>>>>>> What files will i work with? jbrowse.conf or tracks.conf or hard >>>>>>>> code. >>>>>>>> >>>>>>>> On Tue, Oct 23, 2018 at 7:47 PM Garrett Stevens < >>>>>>>> ste...@gm...> wrote: >>>>>>>> >>>>>>>>> Either should work, as long as you specify the paths to the files >>>>>>>>> correctly. E.g. >>>>>>>>> >>>>>>>>> cd /var/www/html/jbrowse >>>>>>>>> bgzip data/volvox.sorted.gff3 tabix -p gff >>>>>>>>> data/volvox.sorted.gff3.gz >>>>>>>>> >>>>>>>>> and >>>>>>>>> >>>>>>>>> cd /var/www/html/jbrowse/data >>>>>>>>> bgzip volvox.sorted.gff3 tabix -p gff volvox.sorted.gff3.gz >>>>>>>>> >>>>>>>>> should both work. >>>>>>>>> >>>>>>>>> ~Garrett >>>>>>>>> >>>>>>>>> On Tue, Oct 23, 2018 at 12:00 PM Beatrice Kodero < >>>>>>>>> kod...@gm...> wrote: >>>>>>>>> >>>>>>>>>> thanks for your mail again, >>>>>>>>>> >>>>>>>>>> kindly clarify should I be /var/www/html/jbrowse/data or >>>>>>>>>> /var/www/html/jbrowse >>>>>>>>>> >>>>>>>>>> Been working from /var/www/html/jbrowse/data to install content >>>>>>>>>> of https://jbrowse.org/docs/tutorial.html ie FASTA, GFF3 >>>>>>>>>> >>>>>>>>>> Thanks >>>>>>>>>> >>>>>>>>>> On Tue, Oct 23, 2018 at 6:50 PM Garrett Stevens < >>>>>>>>>> ste...@gm...> wrote: >>>>>>>>>> >>>>>>>>>>> Ok, so looking at the error in your first message, it looks like >>>>>>>>>>> you perhaps weren't in the right location when you ran the bgzip and tabix >>>>>>>>>>> commands. Those are the commands that will generate the files you are >>>>>>>>>>> missing. Try making sure you cd to the right directory first, >>>>>>>>>>> like: >>>>>>>>>>> >>>>>>>>>>> cd /var/www/html/jbrowse >>>>>>>>>>> bgzip data/volvox.sorted.gff3 tabix -p gff >>>>>>>>>>> data/volvox.sorted.gff3.gz >>>>>>>>>>> >>>>>>>>>>> ~Garrett >>>>>>>>>>> >>>>>>>>>>> On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero < >>>>>>>>>>> kod...@gm...> wrote: >>>>>>>>>>> >>>>>>>>>>>> Thanks for apt response Garrett >>>>>>>>>>>> >>>>>>>>>>>> I am following step step process on the link http://jbrowse.org/docs/installation.html >>>>>>>>>>>> . >>>>>>>>>>>> >>>>>>>>>>>> <http://jbrowse.org/docs/installation.html> >>>>>>>>>>>> I used wget and downloaded above. The challenge am facing >>>>>>>>>>>> begins at http://jbrowse.org/docs/tutorial.html >>>>>>>>>>>> >>>>>>>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa >>>>>>>>>>>> >>>>>>>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 >>>>>>>>>>>> >>>>>>>>>>>> I only got these files >>>>>>>>>>>> tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 >>>>>>>>>>>> >>>>>>>>>>>> Instead of below files >>>>>>>>>>>> /var/www/html/jbrowse >>>>>>>>>>>> /var/www/html/jbrowse/data >>>>>>>>>>>> /var/www/html/jbrowse/data/volvox.fa >>>>>>>>>>>> /var/www/html/jbrowse/data/volvox.fa.fai >>>>>>>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz >>>>>>>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi >>>>>>>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam >>>>>>>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam.bai >>>>>>>>>>>> /var/www/html/jbrowse/data/tracks.conf >>>>>>>>>>>> >>>>>>>>>>>> I am missing >>>>>>>>>>>> >>>>>>>>>>>> volvox.sorted.gff3.gz >>>>>>>>>>>> >>>>>>>>>>>> volvox.sorted.gff3.gz.tbi >>>>>>>>>>>> >>>>>>>>>>>> Kindly advise. >>>>>>>>>>>> >>>>>>>>>>>> Regards >>>>>>>>>>>> >>>>>>>>>>>> Beatrice >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens < >>>>>>>>>>>> ste...@gm...> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hello, >>>>>>>>>>>>> >>>>>>>>>>>>> When you say the curl link is not working, what do you mean? >>>>>>>>>>>>> Are you using the installation instructions found here >>>>>>>>>>>>> <http://jbrowse.org/docs/installation.html>? I tried the curl >>>>>>>>>>>>> command on that page and it worked fine for me: >>>>>>>>>>>>> >>>>>>>>>>>>> curl -O >>>>>>>>>>>>> https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >>>>>>>>>>>>> >>>>>>>>>>>>> Also the output you pasted was something with bgzip, not curl, >>>>>>>>>>>>> so I'm not sure what the problem is there. If you can give some more detail >>>>>>>>>>>>> we can see if we can help. >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> Garrett >>>>>>>>>>>>> >>>>>>>>>>>>> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero < >>>>>>>>>>>>> kod...@gm...> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi , >>>>>>>>>>>>>> >>>>>>>>>>>>>> I trust that this email finds you well. >>>>>>>>>>>>>> >>>>>>>>>>>>>> I am at the point of installing jbowse and the curl link is >>>>>>>>>>>>>> not working. see below installation >>>>>>>>>>>>>> >>>>>>>>>>>>>> bgzip data/volvox.sorted.gff3 >>>>>>>>>>>>>> >>>>>>>>>>>>>> [bgzip] No such file or directory: >>>>>>>>>>>>>> data/volvox.sorted.gff3...........error am getting. >>>>>>>>>>>>>> >>>>>>>>>>>>>> What could i be doing wrong? >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> >>>>>>>>>>>>>> Regards, >>>>>>>>>>>>>> Beatrice Kodero >>>>>>>>>>>>>> >>>>>>>>>>>>>> "Winning means you're willing to go longer, work harder, and >>>>>>>>>>>>>> give more than anyone else." Vince Lombardi >>>>>>>>>>>>>> >>>>>>>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>>>>>>> Skype : B.Kodero >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Gmod-ajax mailing list >>>>>>>>>>>>>> Gmo...@li... >>>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> Regards, >>>>>>>>>>>> Beatrice Kodero >>>>>>>>>>>> >>>>>>>>>>>> "Winning means you're willing to go longer, work harder, and >>>>>>>>>>>> give more than anyone else." Vince Lombardi >>>>>>>>>>>> >>>>>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>>>>> Skype : B.Kodero >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> Regards, >>>>>>>>>> Beatrice Kodero >>>>>>>>>> >>>>>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>>>>> more than anyone else." Vince Lombardi >>>>>>>>>> >>>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>>> Skype : B.Kodero >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> Regards, >>>>>>>> Beatrice Kodero >>>>>>>> >>>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>>> more than anyone else." Vince Lombardi >>>>>>>> >>>>>>>> Mobile : +254 726 486 077 >>>>>>>> Skype : B.Kodero >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> Regards, >>>>>>> Beatrice Kodero >>>>>>> >>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>> more than anyone else." Vince Lombardi >>>>>>> >>>>>>> Mobile : +254 726 486 077 >>>>>>> Skype : B.Kodero >>>>>>> >>>>>>> <WhatsApp Image 2018-10-23 at 8.28.07 PM(1).jpeg> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Gmod-ajax mailing list >>>>>>> Gmo...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>>> >>>>>>> >> >> -- >> >> Regards, >> Beatrice Kodero >> >> "Winning means you're willing to go longer, work harder, and give more >> than anyone else." Vince Lombardi >> >> Mobile : +254 726 486 077 >> Skype : B.Kodero >> > -- Regards, Beatrice Kodero "Winning means you're willing to go longer, work harder, and give more than anyone else." Vince Lombardi Mobile : +254 726 486 077 Skype : B.Kodero |
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From: Ke J. <bio...@gm...> - 2018-10-25 17:42:49
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My solution to the scaling problem was to scale them before JBrowse: when converting BAM or whatever other format to BigWig I supplied a scaling factor based on mapped reads. This way, for one experiment, all BigWig coverage are "normalized" across the board. When viewing them as individual tracks on JBrowse, you'll get a normalized view and could compare across samples. On Thu, Oct 25, 2018 at 12:29 PM Vaneet Lotay <van...@uc...> wrote: > Thanks for the tip, already have that plugin installed and it is the > closest thing to my request so far. However it would nice to just have it > so that you can graph bigwigs in the traditional bigwig XY plot format. > The multibigwig plugin does have an XYplot option but it has no legend for > each track and graph color. Also I mean to graph all tracks separately in > their own track lines as opposed to graphing them all together on the same > physical space. This does work though as a good temporary measure until a > new feature can be added to JBrowse. > > > > Vaneet > > > > *Vaneet Lotay* > > *Xenbase Bioinformatician* > > *716 ICT Building - University of Calgary* > > *2500 University Drive NW* > > *Calgary AB T2N 1N4* > > *CANADA* > > > > *From:* Ke Jiang [mailto:bio...@gm...] > *Sent:* Thursday, October 25, 2018 11:25 AM > *To:* Vaneet Lotay <van...@uc...> > *Cc:* gmo...@li... > *Subject:* Re: [Gmod-ajax] JBrowse scale tracks together > > > > Would this help? > > > > https://github.com/elsiklab/multibigwig > > > > On Thu, Oct 25, 2018 at 12:10 PM Vaneet Lotay <van...@uc...> > wrote: > > Hello all, > > > > I am wondering if there’s a feature or plugin in JBrowse that allows you > to view bigwig tracks together in a group that will allow you to scale them > together when viewing them in a browser. When I say scale them together, I > don’t necessarily mean they all have the same maximum value for their > graphs, but that whichever scaling you choose (local, global, max,…) that > it’s common among all tracks in the group. > > > > I think this is greatly needed because unless you set each bigwig track to > the same maximum scale manually, comparing tracks together which are > locally or globally scaled can be tough as more often than not they have > different scales for their Y axes. > > > > So I’m not sure if there’s a way to make track groups like this for this > purpose, if not, please add this request for the next JBrowse release if > you feel this is necessary. > > > > I really appreciate you adding the sorting of track categories, so > impressed with how quickly you guys post new JBrowse releases as well as > adding user requests. I wouldn’t really begin to know how you can add a > feature for custom sorting tracks within a category, but would that be > possible to add in a future release somehow? Maybe an orderID of some sort > perhaps? > > > > Thanks, > > > > Vaneet > > > > *Vaneet Lotay* > > *Xenbase Bioinformatician* > > *716 ICT Building – University of Calgary* > > *2500 University Drive NW* > > *Calgary, AB T2N 1N4* > > *CANADA* > > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > |
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From: Vaneet L. <van...@uc...> - 2018-10-25 17:29:30
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Thanks for the tip, already have that plugin installed and it is the closest thing to my request so far. However it would nice to just have it so that you can graph bigwigs in the traditional bigwig XY plot format. The multibigwig plugin does have an XYplot option but it has no legend for each track and graph color. Also I mean to graph all tracks separately in their own track lines as opposed to graphing them all together on the same physical space. This does work though as a good temporary measure until a new feature can be added to JBrowse. Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building - University of Calgary 2500 University Drive NW Calgary AB T2N 1N4 CANADA From: Ke Jiang [mailto:bio...@gm...] Sent: Thursday, October 25, 2018 11:25 AM To: Vaneet Lotay <van...@uc...> Cc: gmo...@li... Subject: Re: [Gmod-ajax] JBrowse scale tracks together Would this help? https://github.com/elsiklab/multibigwig On Thu, Oct 25, 2018 at 12:10 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote: Hello all, I am wondering if there’s a feature or plugin in JBrowse that allows you to view bigwig tracks together in a group that will allow you to scale them together when viewing them in a browser. When I say scale them together, I don’t necessarily mean they all have the same maximum value for their graphs, but that whichever scaling you choose (local, global, max,…) that it’s common among all tracks in the group. I think this is greatly needed because unless you set each bigwig track to the same maximum scale manually, comparing tracks together which are locally or globally scaled can be tough as more often than not they have different scales for their Y axes. So I’m not sure if there’s a way to make track groups like this for this purpose, if not, please add this request for the next JBrowse release if you feel this is necessary. I really appreciate you adding the sorting of track categories, so impressed with how quickly you guys post new JBrowse releases as well as adding user requests. I wouldn’t really begin to know how you can add a feature for custom sorting tracks within a category, but would that be possible to add in a future release somehow? Maybe an orderID of some sort perhaps? Thanks, Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building – University of Calgary 2500 University Drive NW Calgary, AB T2N 1N4 CANADA _______________________________________________ Gmod-ajax mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Ke J. <bio...@gm...> - 2018-10-25 17:25:39
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Would this help? https://github.com/elsiklab/multibigwig On Thu, Oct 25, 2018 at 12:10 PM Vaneet Lotay <van...@uc...> wrote: > Hello all, > > > > I am wondering if there’s a feature or plugin in JBrowse that allows you > to view bigwig tracks together in a group that will allow you to scale them > together when viewing them in a browser. When I say scale them together, I > don’t necessarily mean they all have the same maximum value for their > graphs, but that whichever scaling you choose (local, global, max,…) that > it’s common among all tracks in the group. > > > > I think this is greatly needed because unless you set each bigwig track to > the same maximum scale manually, comparing tracks together which are > locally or globally scaled can be tough as more often than not they have > different scales for their Y axes. > > > > So I’m not sure if there’s a way to make track groups like this for this > purpose, if not, please add this request for the next JBrowse release if > you feel this is necessary. > > > > I really appreciate you adding the sorting of track categories, so > impressed with how quickly you guys post new JBrowse releases as well as > adding user requests. I wouldn’t really begin to know how you can add a > feature for custom sorting tracks within a category, but would that be > possible to add in a future release somehow? Maybe an orderID of some sort > perhaps? > > > > Thanks, > > > > Vaneet > > > > *Vaneet Lotay* > > *Xenbase Bioinformatician* > > *716 ICT Building – University of Calgary* > > *2500 University Drive NW* > > *Calgary, AB T2N 1N4* > > *CANADA* > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Vaneet L. <van...@uc...> - 2018-10-25 17:10:03
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Hello all, I am wondering if there's a feature or plugin in JBrowse that allows you to view bigwig tracks together in a group that will allow you to scale them together when viewing them in a browser. When I say scale them together, I don't necessarily mean they all have the same maximum value for their graphs, but that whichever scaling you choose (local, global, max,...) that it's common among all tracks in the group. I think this is greatly needed because unless you set each bigwig track to the same maximum scale manually, comparing tracks together which are locally or globally scaled can be tough as more often than not they have different scales for their Y axes. So I'm not sure if there's a way to make track groups like this for this purpose, if not, please add this request for the next JBrowse release if you feel this is necessary. I really appreciate you adding the sorting of track categories, so impressed with how quickly you guys post new JBrowse releases as well as adding user requests. I wouldn't really begin to know how you can add a feature for custom sorting tracks within a category, but would that be possible to add in a future release somehow? Maybe an orderID of some sort perhaps? Thanks, Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building - University of Calgary 2500 University Drive NW Calgary, AB T2N 1N4 CANADA |
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From: Garrett S. <ste...@gm...> - 2018-10-24 19:02:26
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The desktop version should be able to open VCF files. I was just able to open one on my computer. If you let us know what you have tried and what error you got, maybe we can help. ~Garrett On Wed, Oct 24, 2018 at 2:56 PM Beatrice Kodero <kod...@gm...> wrote: > Thanks for your continued support. I heartily appreciate. > > Desktop was my choice but could not load VCF files > > On Wed, Oct 24, 2018 at 5:09 PM Garrett Stevens < > ste...@gm...> wrote: > >> The general idea is to put the data you want to visualize in the data >> directory (probably /var/www/html/jbrowse/data for you) and then add >> track entries that reference that data to either tracks.conf or >> trackList.json in the data directory. Either the conf or json files >> work, they can do the same things. >> >> For reference, the configuration files for that site you linked can be >> viewed at http://jbrowse.igs.umaryland.edu/t_parva/data/trackList.json >> and http://jbrowse.igs.umaryland.edu/t_parva/data/tracks.conf. There are >> lots of different types of tracks, so to configure the specific types of >> tracks you want you'll have to look at our documentation >> <http://jbrowse.org/docs/reference_sequence.html> under "Configuring >> Tracks." >> >> Another option if you're only viewing locally is JBrowse Desktop >> <http://jbrowse.org/docs/jbrowse_desktop.html>, which can load your data >> and then save your session so you can come back to the same data later. >> >> ~Garrett >> >> On Tue, Oct 23, 2018 at 8:49 PM Beatrice Kodero <kod...@gm...> >> wrote: >> >>> I am new to Linux and this is my first system to install. >>> >>> Would like to customise , have day preloaded ( like link sent before) >>> and visualize data locally of T.parva genomes >>> >>> Apologies for to many questions ;-) >>> >>> On Wed, Oct 24, 2018, 2:44 AM Beatrice Kodero <kod...@gm...> >>> wrote: >>> >>>> >>>> Please allow me to ask, After installation and I want to preload data >>>> to my localhost ie i don't have to upload a reference gene or add track >>>> something like this here >>>> >>>> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >>>> What files will i work with? jbrowse.conf or tracks.conf or hard code? >>>> >>>> Regards >>>> Beatrice >>>> >>>> On Tue, Oct 23, 2018, 9:40 PM Beatrice Kodero <kod...@gm...> >>>> wrote: >>>> >>>>> Hey Scott, >>>>> >>>>> It's blank >>>>> >>>>> On Tue, Oct 23, 2018, 9:06 PM Scott Cain <sc...@sc...> wrote: >>>>> >>>>>> Hi Beatrice, >>>>>> >>>>>> I can’t quite make out the text in the red bar (where the error >>>>>> message is). Can you tell us what it says? >>>>>> >>>>>> Thanks, Scott >>>>>> >>>>>> On Oct 23, 2018, at 10:31 AM, Beatrice Kodero <kod...@gm...> >>>>>> wrote: >>>>>> >>>>>> Please find attached. The error I am now getting from installation >>>>>> >>>>>> On Tue, Oct 23, 2018 at 8:21 PM Beatrice Kodero <kod...@gm...> >>>>>> wrote: >>>>>> >>>>>>> Garrett Thanks a million. >>>>>>> >>>>>>> Able to download at cd/var/www/html/jbrowse >>>>>>> >>>>>>> Please allow me to ask, After installation and I want to preload >>>>>>> data to my localhost ie i don't have to upload a reference gene or add >>>>>>> track something like this here >>>>>>> >>>>>>> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >>>>>>> What files will i work with? jbrowse.conf or tracks.conf or hard >>>>>>> code. >>>>>>> >>>>>>> On Tue, Oct 23, 2018 at 7:47 PM Garrett Stevens < >>>>>>> ste...@gm...> wrote: >>>>>>> >>>>>>>> Either should work, as long as you specify the paths to the files >>>>>>>> correctly. E.g. >>>>>>>> >>>>>>>> cd /var/www/html/jbrowse >>>>>>>> bgzip data/volvox.sorted.gff3 tabix -p gff >>>>>>>> data/volvox.sorted.gff3.gz >>>>>>>> >>>>>>>> and >>>>>>>> >>>>>>>> cd /var/www/html/jbrowse/data >>>>>>>> bgzip volvox.sorted.gff3 tabix -p gff volvox.sorted.gff3.gz >>>>>>>> >>>>>>>> should both work. >>>>>>>> >>>>>>>> ~Garrett >>>>>>>> >>>>>>>> On Tue, Oct 23, 2018 at 12:00 PM Beatrice Kodero < >>>>>>>> kod...@gm...> wrote: >>>>>>>> >>>>>>>>> thanks for your mail again, >>>>>>>>> >>>>>>>>> kindly clarify should I be /var/www/html/jbrowse/data or >>>>>>>>> /var/www/html/jbrowse >>>>>>>>> >>>>>>>>> Been working from /var/www/html/jbrowse/data to install content of >>>>>>>>> https://jbrowse.org/docs/tutorial.html ie FASTA, GFF3 >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> On Tue, Oct 23, 2018 at 6:50 PM Garrett Stevens < >>>>>>>>> ste...@gm...> wrote: >>>>>>>>> >>>>>>>>>> Ok, so looking at the error in your first message, it looks like >>>>>>>>>> you perhaps weren't in the right location when you ran the bgzip and tabix >>>>>>>>>> commands. Those are the commands that will generate the files you are >>>>>>>>>> missing. Try making sure you cd to the right directory first, >>>>>>>>>> like: >>>>>>>>>> >>>>>>>>>> cd /var/www/html/jbrowse >>>>>>>>>> bgzip data/volvox.sorted.gff3 tabix -p gff >>>>>>>>>> data/volvox.sorted.gff3.gz >>>>>>>>>> >>>>>>>>>> ~Garrett >>>>>>>>>> >>>>>>>>>> On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero < >>>>>>>>>> kod...@gm...> wrote: >>>>>>>>>> >>>>>>>>>>> Thanks for apt response Garrett >>>>>>>>>>> >>>>>>>>>>> I am following step step process on the link http://jbrowse.org/docs/installation.html >>>>>>>>>>> . >>>>>>>>>>> >>>>>>>>>>> <http://jbrowse.org/docs/installation.html> >>>>>>>>>>> I used wget and downloaded above. The challenge am facing begins >>>>>>>>>>> at http://jbrowse.org/docs/tutorial.html >>>>>>>>>>> >>>>>>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa >>>>>>>>>>> >>>>>>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 >>>>>>>>>>> >>>>>>>>>>> I only got these files >>>>>>>>>>> tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 >>>>>>>>>>> >>>>>>>>>>> Instead of below files >>>>>>>>>>> /var/www/html/jbrowse >>>>>>>>>>> /var/www/html/jbrowse/data >>>>>>>>>>> /var/www/html/jbrowse/data/volvox.fa >>>>>>>>>>> /var/www/html/jbrowse/data/volvox.fa.fai >>>>>>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz >>>>>>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi >>>>>>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam >>>>>>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam.bai >>>>>>>>>>> /var/www/html/jbrowse/data/tracks.conf >>>>>>>>>>> >>>>>>>>>>> I am missing >>>>>>>>>>> >>>>>>>>>>> volvox.sorted.gff3.gz >>>>>>>>>>> >>>>>>>>>>> volvox.sorted.gff3.gz.tbi >>>>>>>>>>> >>>>>>>>>>> Kindly advise. >>>>>>>>>>> >>>>>>>>>>> Regards >>>>>>>>>>> >>>>>>>>>>> Beatrice >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens < >>>>>>>>>>> ste...@gm...> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hello, >>>>>>>>>>>> >>>>>>>>>>>> When you say the curl link is not working, what do you mean? >>>>>>>>>>>> Are you using the installation instructions found here >>>>>>>>>>>> <http://jbrowse.org/docs/installation.html>? I tried the curl >>>>>>>>>>>> command on that page and it worked fine for me: >>>>>>>>>>>> >>>>>>>>>>>> curl -O >>>>>>>>>>>> https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >>>>>>>>>>>> >>>>>>>>>>>> Also the output you pasted was something with bgzip, not curl, >>>>>>>>>>>> so I'm not sure what the problem is there. If you can give some more detail >>>>>>>>>>>> we can see if we can help. >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Garrett >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero < >>>>>>>>>>>> kod...@gm...> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi , >>>>>>>>>>>>> >>>>>>>>>>>>> I trust that this email finds you well. >>>>>>>>>>>>> >>>>>>>>>>>>> I am at the point of installing jbowse and the curl link is >>>>>>>>>>>>> not working. see below installation >>>>>>>>>>>>> >>>>>>>>>>>>> bgzip data/volvox.sorted.gff3 >>>>>>>>>>>>> >>>>>>>>>>>>> [bgzip] No such file or directory: >>>>>>>>>>>>> data/volvox.sorted.gff3...........error am getting. >>>>>>>>>>>>> >>>>>>>>>>>>> What could i be doing wrong? >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> >>>>>>>>>>>>> Regards, >>>>>>>>>>>>> Beatrice Kodero >>>>>>>>>>>>> >>>>>>>>>>>>> "Winning means you're willing to go longer, work harder, and >>>>>>>>>>>>> give more than anyone else." Vince Lombardi >>>>>>>>>>>>> >>>>>>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>>>>>> Skype : B.Kodero >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Gmod-ajax mailing list >>>>>>>>>>>>> Gmo...@li... >>>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> Regards, >>>>>>>>>>> Beatrice Kodero >>>>>>>>>>> >>>>>>>>>>> "Winning means you're willing to go longer, work harder, and >>>>>>>>>>> give more than anyone else." Vince Lombardi >>>>>>>>>>> >>>>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>>>> Skype : B.Kodero >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> Regards, >>>>>>>>> Beatrice Kodero >>>>>>>>> >>>>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>>>> more than anyone else." Vince Lombardi >>>>>>>>> >>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>> Skype : B.Kodero >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> Regards, >>>>>>> Beatrice Kodero >>>>>>> >>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>> more than anyone else." Vince Lombardi >>>>>>> >>>>>>> Mobile : +254 726 486 077 >>>>>>> Skype : B.Kodero >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> Regards, >>>>>> Beatrice Kodero >>>>>> >>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>> more than anyone else." Vince Lombardi >>>>>> >>>>>> Mobile : +254 726 486 077 >>>>>> Skype : B.Kodero >>>>>> >>>>>> <WhatsApp Image 2018-10-23 at 8.28.07 PM(1).jpeg> >>>>>> >>>>>> _______________________________________________ >>>>>> Gmod-ajax mailing list >>>>>> Gmo...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>> >>>>>> > > -- > > Regards, > Beatrice Kodero > > "Winning means you're willing to go longer, work harder, and give more > than anyone else." Vince Lombardi > > Mobile : +254 726 486 077 > Skype : B.Kodero > |
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From: Beatrice K. <kod...@gm...> - 2018-10-24 18:56:28
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Thanks for your continued support. I heartily appreciate. Desktop was my choice but could not load VCF files On Wed, Oct 24, 2018 at 5:09 PM Garrett Stevens <ste...@gm...> wrote: > The general idea is to put the data you want to visualize in the data > directory (probably /var/www/html/jbrowse/data for you) and then add > track entries that reference that data to either tracks.conf or > trackList.json in the data directory. Either the conf or json files work, > they can do the same things. > > For reference, the configuration files for that site you linked can be > viewed at http://jbrowse.igs.umaryland.edu/t_parva/data/trackList.json > and http://jbrowse.igs.umaryland.edu/t_parva/data/tracks.conf. There are > lots of different types of tracks, so to configure the specific types of > tracks you want you'll have to look at our documentation > <http://jbrowse.org/docs/reference_sequence.html> under "Configuring > Tracks." > > Another option if you're only viewing locally is JBrowse Desktop > <http://jbrowse.org/docs/jbrowse_desktop.html>, which can load your data > and then save your session so you can come back to the same data later. > > ~Garrett > > On Tue, Oct 23, 2018 at 8:49 PM Beatrice Kodero <kod...@gm...> > wrote: > >> I am new to Linux and this is my first system to install. >> >> Would like to customise , have day preloaded ( like link sent before) and >> visualize data locally of T.parva genomes >> >> Apologies for to many questions ;-) >> >> On Wed, Oct 24, 2018, 2:44 AM Beatrice Kodero <kod...@gm...> >> wrote: >> >>> >>> Please allow me to ask, After installation and I want to preload data to >>> my localhost ie i don't have to upload a reference gene or add track >>> something like this here >>> >>> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >>> What files will i work with? jbrowse.conf or tracks.conf or hard code? >>> >>> Regards >>> Beatrice >>> >>> On Tue, Oct 23, 2018, 9:40 PM Beatrice Kodero <kod...@gm...> >>> wrote: >>> >>>> Hey Scott, >>>> >>>> It's blank >>>> >>>> On Tue, Oct 23, 2018, 9:06 PM Scott Cain <sc...@sc...> wrote: >>>> >>>>> Hi Beatrice, >>>>> >>>>> I can’t quite make out the text in the red bar (where the error >>>>> message is). Can you tell us what it says? >>>>> >>>>> Thanks, Scott >>>>> >>>>> On Oct 23, 2018, at 10:31 AM, Beatrice Kodero <kod...@gm...> >>>>> wrote: >>>>> >>>>> Please find attached. The error I am now getting from installation >>>>> >>>>> On Tue, Oct 23, 2018 at 8:21 PM Beatrice Kodero <kod...@gm...> >>>>> wrote: >>>>> >>>>>> Garrett Thanks a million. >>>>>> >>>>>> Able to download at cd/var/www/html/jbrowse >>>>>> >>>>>> Please allow me to ask, After installation and I want to preload data >>>>>> to my localhost ie i don't have to upload a reference gene or add track >>>>>> something like this here >>>>>> >>>>>> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >>>>>> What files will i work with? jbrowse.conf or tracks.conf or hard code. >>>>>> >>>>>> On Tue, Oct 23, 2018 at 7:47 PM Garrett Stevens < >>>>>> ste...@gm...> wrote: >>>>>> >>>>>>> Either should work, as long as you specify the paths to the files >>>>>>> correctly. E.g. >>>>>>> >>>>>>> cd /var/www/html/jbrowse >>>>>>> bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz >>>>>>> >>>>>>> and >>>>>>> >>>>>>> cd /var/www/html/jbrowse/data >>>>>>> bgzip volvox.sorted.gff3 tabix -p gff volvox.sorted.gff3.gz >>>>>>> >>>>>>> should both work. >>>>>>> >>>>>>> ~Garrett >>>>>>> >>>>>>> On Tue, Oct 23, 2018 at 12:00 PM Beatrice Kodero < >>>>>>> kod...@gm...> wrote: >>>>>>> >>>>>>>> thanks for your mail again, >>>>>>>> >>>>>>>> kindly clarify should I be /var/www/html/jbrowse/data or >>>>>>>> /var/www/html/jbrowse >>>>>>>> >>>>>>>> Been working from /var/www/html/jbrowse/data to install content of >>>>>>>> https://jbrowse.org/docs/tutorial.html ie FASTA, GFF3 >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> On Tue, Oct 23, 2018 at 6:50 PM Garrett Stevens < >>>>>>>> ste...@gm...> wrote: >>>>>>>> >>>>>>>>> Ok, so looking at the error in your first message, it looks like >>>>>>>>> you perhaps weren't in the right location when you ran the bgzip and tabix >>>>>>>>> commands. Those are the commands that will generate the files you are >>>>>>>>> missing. Try making sure you cd to the right directory first, >>>>>>>>> like: >>>>>>>>> >>>>>>>>> cd /var/www/html/jbrowse >>>>>>>>> bgzip data/volvox.sorted.gff3 tabix -p gff >>>>>>>>> data/volvox.sorted.gff3.gz >>>>>>>>> >>>>>>>>> ~Garrett >>>>>>>>> >>>>>>>>> On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero < >>>>>>>>> kod...@gm...> wrote: >>>>>>>>> >>>>>>>>>> Thanks for apt response Garrett >>>>>>>>>> >>>>>>>>>> I am following step step process on the link http://jbrowse.org/docs/installation.html >>>>>>>>>> . >>>>>>>>>> >>>>>>>>>> <http://jbrowse.org/docs/installation.html> >>>>>>>>>> I used wget and downloaded above. The challenge am facing begins >>>>>>>>>> at http://jbrowse.org/docs/tutorial.html >>>>>>>>>> >>>>>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa >>>>>>>>>> >>>>>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 >>>>>>>>>> >>>>>>>>>> I only got these files >>>>>>>>>> tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 >>>>>>>>>> >>>>>>>>>> Instead of below files >>>>>>>>>> /var/www/html/jbrowse >>>>>>>>>> /var/www/html/jbrowse/data >>>>>>>>>> /var/www/html/jbrowse/data/volvox.fa >>>>>>>>>> /var/www/html/jbrowse/data/volvox.fa.fai >>>>>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz >>>>>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi >>>>>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam >>>>>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam.bai >>>>>>>>>> /var/www/html/jbrowse/data/tracks.conf >>>>>>>>>> >>>>>>>>>> I am missing >>>>>>>>>> >>>>>>>>>> volvox.sorted.gff3.gz >>>>>>>>>> >>>>>>>>>> volvox.sorted.gff3.gz.tbi >>>>>>>>>> >>>>>>>>>> Kindly advise. >>>>>>>>>> >>>>>>>>>> Regards >>>>>>>>>> >>>>>>>>>> Beatrice >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens < >>>>>>>>>> ste...@gm...> wrote: >>>>>>>>>> >>>>>>>>>>> Hello, >>>>>>>>>>> >>>>>>>>>>> When you say the curl link is not working, what do you mean? Are >>>>>>>>>>> you using the installation instructions found here >>>>>>>>>>> <http://jbrowse.org/docs/installation.html>? I tried the curl >>>>>>>>>>> command on that page and it worked fine for me: >>>>>>>>>>> >>>>>>>>>>> curl -O >>>>>>>>>>> https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >>>>>>>>>>> >>>>>>>>>>> Also the output you pasted was something with bgzip, not curl, >>>>>>>>>>> so I'm not sure what the problem is there. If you can give some more detail >>>>>>>>>>> we can see if we can help. >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> Garrett >>>>>>>>>>> >>>>>>>>>>> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero < >>>>>>>>>>> kod...@gm...> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi , >>>>>>>>>>>> >>>>>>>>>>>> I trust that this email finds you well. >>>>>>>>>>>> >>>>>>>>>>>> I am at the point of installing jbowse and the curl link is not >>>>>>>>>>>> working. see below installation >>>>>>>>>>>> >>>>>>>>>>>> bgzip data/volvox.sorted.gff3 >>>>>>>>>>>> >>>>>>>>>>>> [bgzip] No such file or directory: >>>>>>>>>>>> data/volvox.sorted.gff3...........error am getting. >>>>>>>>>>>> >>>>>>>>>>>> What could i be doing wrong? >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> >>>>>>>>>>>> Regards, >>>>>>>>>>>> Beatrice Kodero >>>>>>>>>>>> >>>>>>>>>>>> "Winning means you're willing to go longer, work harder, and >>>>>>>>>>>> give more than anyone else." Vince Lombardi >>>>>>>>>>>> >>>>>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>>>>> Skype : B.Kodero >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Gmod-ajax mailing list >>>>>>>>>>>> Gmo...@li... >>>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> Regards, >>>>>>>>>> Beatrice Kodero >>>>>>>>>> >>>>>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>>>>> more than anyone else." Vince Lombardi >>>>>>>>>> >>>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>>> Skype : B.Kodero >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> Regards, >>>>>>>> Beatrice Kodero >>>>>>>> >>>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>>> more than anyone else." Vince Lombardi >>>>>>>> >>>>>>>> Mobile : +254 726 486 077 >>>>>>>> Skype : B.Kodero >>>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> Regards, >>>>>> Beatrice Kodero >>>>>> >>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>> more than anyone else." Vince Lombardi >>>>>> >>>>>> Mobile : +254 726 486 077 >>>>>> Skype : B.Kodero >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> Regards, >>>>> Beatrice Kodero >>>>> >>>>> "Winning means you're willing to go longer, work harder, and give more >>>>> than anyone else." Vince Lombardi >>>>> >>>>> Mobile : +254 726 486 077 >>>>> Skype : B.Kodero >>>>> >>>>> <WhatsApp Image 2018-10-23 at 8.28.07 PM(1).jpeg> >>>>> >>>>> _______________________________________________ >>>>> Gmod-ajax mailing list >>>>> Gmo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>> >>>>> -- Regards, Beatrice Kodero "Winning means you're willing to go longer, work harder, and give more than anyone else." Vince Lombardi Mobile : +254 726 486 077 Skype : B.Kodero |
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From: Garrett S. <ste...@gm...> - 2018-10-24 14:09:57
|
The general idea is to put the data you want to visualize in the data directory (probably /var/www/html/jbrowse/data for you) and then add track entries that reference that data to either tracks.conf or trackList.json in the data directory. Either the conf or json files work, they can do the same things. For reference, the configuration files for that site you linked can be viewed at http://jbrowse.igs.umaryland.edu/t_parva/data/trackList.json and http://jbrowse.igs.umaryland.edu/t_parva/data/tracks.conf. There are lots of different types of tracks, so to configure the specific types of tracks you want you'll have to look at our documentation <http://jbrowse.org/docs/reference_sequence.html> under "Configuring Tracks." Another option if you're only viewing locally is JBrowse Desktop <http://jbrowse.org/docs/jbrowse_desktop.html>, which can load your data and then save your session so you can come back to the same data later. ~Garrett On Tue, Oct 23, 2018 at 8:49 PM Beatrice Kodero <kod...@gm...> wrote: > I am new to Linux and this is my first system to install. > > Would like to customise , have day preloaded ( like link sent before) and > visualize data locally of T.parva genomes > > Apologies for to many questions ;-) > > On Wed, Oct 24, 2018, 2:44 AM Beatrice Kodero <kod...@gm...> wrote: > >> >> Please allow me to ask, After installation and I want to preload data to >> my localhost ie i don't have to upload a reference gene or add track >> something like this here >> >> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >> What files will i work with? jbrowse.conf or tracks.conf or hard code? >> >> Regards >> Beatrice >> >> On Tue, Oct 23, 2018, 9:40 PM Beatrice Kodero <kod...@gm...> >> wrote: >> >>> Hey Scott, >>> >>> It's blank >>> >>> On Tue, Oct 23, 2018, 9:06 PM Scott Cain <sc...@sc...> wrote: >>> >>>> Hi Beatrice, >>>> >>>> I can’t quite make out the text in the red bar (where the error message >>>> is). Can you tell us what it says? >>>> >>>> Thanks, Scott >>>> >>>> On Oct 23, 2018, at 10:31 AM, Beatrice Kodero <kod...@gm...> >>>> wrote: >>>> >>>> Please find attached. The error I am now getting from installation >>>> >>>> On Tue, Oct 23, 2018 at 8:21 PM Beatrice Kodero <kod...@gm...> >>>> wrote: >>>> >>>>> Garrett Thanks a million. >>>>> >>>>> Able to download at cd/var/www/html/jbrowse >>>>> >>>>> Please allow me to ask, After installation and I want to preload data >>>>> to my localhost ie i don't have to upload a reference gene or add track >>>>> something like this here >>>>> >>>>> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >>>>> What files will i work with? jbrowse.conf or tracks.conf or hard code. >>>>> >>>>> On Tue, Oct 23, 2018 at 7:47 PM Garrett Stevens < >>>>> ste...@gm...> wrote: >>>>> >>>>>> Either should work, as long as you specify the paths to the files >>>>>> correctly. E.g. >>>>>> >>>>>> cd /var/www/html/jbrowse >>>>>> bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz >>>>>> >>>>>> and >>>>>> >>>>>> cd /var/www/html/jbrowse/data >>>>>> bgzip volvox.sorted.gff3 tabix -p gff volvox.sorted.gff3.gz >>>>>> >>>>>> should both work. >>>>>> >>>>>> ~Garrett >>>>>> >>>>>> On Tue, Oct 23, 2018 at 12:00 PM Beatrice Kodero <kod...@gm...> >>>>>> wrote: >>>>>> >>>>>>> thanks for your mail again, >>>>>>> >>>>>>> kindly clarify should I be /var/www/html/jbrowse/data or >>>>>>> /var/www/html/jbrowse >>>>>>> >>>>>>> Been working from /var/www/html/jbrowse/data to install content of >>>>>>> https://jbrowse.org/docs/tutorial.html ie FASTA, GFF3 >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> On Tue, Oct 23, 2018 at 6:50 PM Garrett Stevens < >>>>>>> ste...@gm...> wrote: >>>>>>> >>>>>>>> Ok, so looking at the error in your first message, it looks like >>>>>>>> you perhaps weren't in the right location when you ran the bgzip and tabix >>>>>>>> commands. Those are the commands that will generate the files you are >>>>>>>> missing. Try making sure you cd to the right directory first, like: >>>>>>>> >>>>>>>> cd /var/www/html/jbrowse >>>>>>>> bgzip data/volvox.sorted.gff3 tabix -p gff >>>>>>>> data/volvox.sorted.gff3.gz >>>>>>>> >>>>>>>> ~Garrett >>>>>>>> >>>>>>>> On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero < >>>>>>>> kod...@gm...> wrote: >>>>>>>> >>>>>>>>> Thanks for apt response Garrett >>>>>>>>> >>>>>>>>> I am following step step process on the link http://jbrowse.org/docs/installation.html >>>>>>>>> . >>>>>>>>> >>>>>>>>> <http://jbrowse.org/docs/installation.html> >>>>>>>>> I used wget and downloaded above. The challenge am facing begins >>>>>>>>> at http://jbrowse.org/docs/tutorial.html >>>>>>>>> >>>>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa >>>>>>>>> >>>>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 >>>>>>>>> >>>>>>>>> I only got these files >>>>>>>>> tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 >>>>>>>>> >>>>>>>>> Instead of below files >>>>>>>>> /var/www/html/jbrowse >>>>>>>>> /var/www/html/jbrowse/data >>>>>>>>> /var/www/html/jbrowse/data/volvox.fa >>>>>>>>> /var/www/html/jbrowse/data/volvox.fa.fai >>>>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz >>>>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi >>>>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam >>>>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam.bai >>>>>>>>> /var/www/html/jbrowse/data/tracks.conf >>>>>>>>> >>>>>>>>> I am missing >>>>>>>>> >>>>>>>>> volvox.sorted.gff3.gz >>>>>>>>> >>>>>>>>> volvox.sorted.gff3.gz.tbi >>>>>>>>> >>>>>>>>> Kindly advise. >>>>>>>>> >>>>>>>>> Regards >>>>>>>>> >>>>>>>>> Beatrice >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens < >>>>>>>>> ste...@gm...> wrote: >>>>>>>>> >>>>>>>>>> Hello, >>>>>>>>>> >>>>>>>>>> When you say the curl link is not working, what do you mean? Are >>>>>>>>>> you using the installation instructions found here >>>>>>>>>> <http://jbrowse.org/docs/installation.html>? I tried the curl >>>>>>>>>> command on that page and it worked fine for me: >>>>>>>>>> >>>>>>>>>> curl -O >>>>>>>>>> https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >>>>>>>>>> >>>>>>>>>> Also the output you pasted was something with bgzip, not curl, so >>>>>>>>>> I'm not sure what the problem is there. If you can give some more detail we >>>>>>>>>> can see if we can help. >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Garrett >>>>>>>>>> >>>>>>>>>> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero < >>>>>>>>>> kod...@gm...> wrote: >>>>>>>>>> >>>>>>>>>>> Hi , >>>>>>>>>>> >>>>>>>>>>> I trust that this email finds you well. >>>>>>>>>>> >>>>>>>>>>> I am at the point of installing jbowse and the curl link is not >>>>>>>>>>> working. see below installation >>>>>>>>>>> >>>>>>>>>>> bgzip data/volvox.sorted.gff3 >>>>>>>>>>> >>>>>>>>>>> [bgzip] No such file or directory: data/volvox.sorted.gff3...........error >>>>>>>>>>> am getting. >>>>>>>>>>> >>>>>>>>>>> What could i be doing wrong? >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> Regards, >>>>>>>>>>> Beatrice Kodero >>>>>>>>>>> >>>>>>>>>>> "Winning means you're willing to go longer, work harder, and >>>>>>>>>>> give more than anyone else." Vince Lombardi >>>>>>>>>>> >>>>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>>>> Skype : B.Kodero >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Gmod-ajax mailing list >>>>>>>>>>> Gmo...@li... >>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> Regards, >>>>>>>>> Beatrice Kodero >>>>>>>>> >>>>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>>>> more than anyone else." Vince Lombardi >>>>>>>>> >>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>> Skype : B.Kodero >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> Regards, >>>>>>> Beatrice Kodero >>>>>>> >>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>> more than anyone else." Vince Lombardi >>>>>>> >>>>>>> Mobile : +254 726 486 077 >>>>>>> Skype : B.Kodero >>>>>>> >>>>>> >>>>> >>>>> -- >>>>> >>>>> Regards, >>>>> Beatrice Kodero >>>>> >>>>> "Winning means you're willing to go longer, work harder, and give more >>>>> than anyone else." Vince Lombardi >>>>> >>>>> Mobile : +254 726 486 077 >>>>> Skype : B.Kodero >>>>> >>>> >>>> >>>> -- >>>> >>>> Regards, >>>> Beatrice Kodero >>>> >>>> "Winning means you're willing to go longer, work harder, and give more >>>> than anyone else." Vince Lombardi >>>> >>>> Mobile : +254 726 486 077 >>>> Skype : B.Kodero >>>> >>>> <WhatsApp Image 2018-10-23 at 8.28.07 PM(1).jpeg> >>>> >>>> _______________________________________________ >>>> Gmod-ajax mailing list >>>> Gmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>> >>>> |
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From: Beatrice K. <kod...@gm...> - 2018-10-24 00:49:43
|
I am new to Linux and this is my first system to install. Would like to customise , have day preloaded ( like link sent before) and visualize data locally of T.parva genomes Apologies for to many questions ;-) On Wed, Oct 24, 2018, 2:44 AM Beatrice Kodero <kod...@gm...> wrote: > > Please allow me to ask, After installation and I want to preload data to > my localhost ie i don't have to upload a reference gene or add track > something like this here > > <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> > What files will i work with? jbrowse.conf or tracks.conf or hard code? > > Regards > Beatrice > > On Tue, Oct 23, 2018, 9:40 PM Beatrice Kodero <kod...@gm...> wrote: > >> Hey Scott, >> >> It's blank >> >> On Tue, Oct 23, 2018, 9:06 PM Scott Cain <sc...@sc...> wrote: >> >>> Hi Beatrice, >>> >>> I can’t quite make out the text in the red bar (where the error message >>> is). Can you tell us what it says? >>> >>> Thanks, Scott >>> >>> On Oct 23, 2018, at 10:31 AM, Beatrice Kodero <kod...@gm...> >>> wrote: >>> >>> Please find attached. The error I am now getting from installation >>> >>> On Tue, Oct 23, 2018 at 8:21 PM Beatrice Kodero <kod...@gm...> >>> wrote: >>> >>>> Garrett Thanks a million. >>>> >>>> Able to download at cd/var/www/html/jbrowse >>>> >>>> Please allow me to ask, After installation and I want to preload data >>>> to my localhost ie i don't have to upload a reference gene or add track >>>> something like this here >>>> >>>> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >>>> What files will i work with? jbrowse.conf or tracks.conf or hard code. >>>> >>>> On Tue, Oct 23, 2018 at 7:47 PM Garrett Stevens < >>>> ste...@gm...> wrote: >>>> >>>>> Either should work, as long as you specify the paths to the files >>>>> correctly. E.g. >>>>> >>>>> cd /var/www/html/jbrowse >>>>> bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz >>>>> >>>>> and >>>>> >>>>> cd /var/www/html/jbrowse/data >>>>> bgzip volvox.sorted.gff3 tabix -p gff volvox.sorted.gff3.gz >>>>> >>>>> should both work. >>>>> >>>>> ~Garrett >>>>> >>>>> On Tue, Oct 23, 2018 at 12:00 PM Beatrice Kodero <kod...@gm...> >>>>> wrote: >>>>> >>>>>> thanks for your mail again, >>>>>> >>>>>> kindly clarify should I be /var/www/html/jbrowse/data or >>>>>> /var/www/html/jbrowse >>>>>> >>>>>> Been working from /var/www/html/jbrowse/data to install content of >>>>>> https://jbrowse.org/docs/tutorial.html ie FASTA, GFF3 >>>>>> >>>>>> Thanks >>>>>> >>>>>> On Tue, Oct 23, 2018 at 6:50 PM Garrett Stevens < >>>>>> ste...@gm...> wrote: >>>>>> >>>>>>> Ok, so looking at the error in your first message, it looks like you >>>>>>> perhaps weren't in the right location when you ran the bgzip and tabix >>>>>>> commands. Those are the commands that will generate the files you are >>>>>>> missing. Try making sure you cd to the right directory first, like: >>>>>>> >>>>>>> cd /var/www/html/jbrowse >>>>>>> bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz >>>>>>> >>>>>>> ~Garrett >>>>>>> >>>>>>> On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero < >>>>>>> kod...@gm...> wrote: >>>>>>> >>>>>>>> Thanks for apt response Garrett >>>>>>>> >>>>>>>> I am following step step process on the link http://jbrowse.org/docs/installation.html >>>>>>>> . >>>>>>>> >>>>>>>> <http://jbrowse.org/docs/installation.html> >>>>>>>> I used wget and downloaded above. The challenge am facing begins at >>>>>>>> http://jbrowse.org/docs/tutorial.html >>>>>>>> >>>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa >>>>>>>> >>>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 >>>>>>>> >>>>>>>> I only got these files >>>>>>>> tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 >>>>>>>> >>>>>>>> Instead of below files >>>>>>>> /var/www/html/jbrowse >>>>>>>> /var/www/html/jbrowse/data >>>>>>>> /var/www/html/jbrowse/data/volvox.fa >>>>>>>> /var/www/html/jbrowse/data/volvox.fa.fai >>>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz >>>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi >>>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam >>>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam.bai >>>>>>>> /var/www/html/jbrowse/data/tracks.conf >>>>>>>> >>>>>>>> I am missing >>>>>>>> >>>>>>>> volvox.sorted.gff3.gz >>>>>>>> >>>>>>>> volvox.sorted.gff3.gz.tbi >>>>>>>> >>>>>>>> Kindly advise. >>>>>>>> >>>>>>>> Regards >>>>>>>> >>>>>>>> Beatrice >>>>>>>> >>>>>>>> >>>>>>>> On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens < >>>>>>>> ste...@gm...> wrote: >>>>>>>> >>>>>>>>> Hello, >>>>>>>>> >>>>>>>>> When you say the curl link is not working, what do you mean? Are >>>>>>>>> you using the installation instructions found here >>>>>>>>> <http://jbrowse.org/docs/installation.html>? I tried the curl >>>>>>>>> command on that page and it worked fine for me: >>>>>>>>> >>>>>>>>> curl -O >>>>>>>>> https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >>>>>>>>> >>>>>>>>> Also the output you pasted was something with bgzip, not curl, so >>>>>>>>> I'm not sure what the problem is there. If you can give some more detail we >>>>>>>>> can see if we can help. >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> Garrett >>>>>>>>> >>>>>>>>> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero < >>>>>>>>> kod...@gm...> wrote: >>>>>>>>> >>>>>>>>>> Hi , >>>>>>>>>> >>>>>>>>>> I trust that this email finds you well. >>>>>>>>>> >>>>>>>>>> I am at the point of installing jbowse and the curl link is not >>>>>>>>>> working. see below installation >>>>>>>>>> >>>>>>>>>> bgzip data/volvox.sorted.gff3 >>>>>>>>>> >>>>>>>>>> [bgzip] No such file or directory: data/volvox.sorted.gff3...........error >>>>>>>>>> am getting. >>>>>>>>>> >>>>>>>>>> What could i be doing wrong? >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> Regards, >>>>>>>>>> Beatrice Kodero >>>>>>>>>> >>>>>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>>>>> more than anyone else." Vince Lombardi >>>>>>>>>> >>>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>>> Skype : B.Kodero >>>>>>>>>> _______________________________________________ >>>>>>>>>> Gmod-ajax mailing list >>>>>>>>>> Gmo...@li... >>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> Regards, >>>>>>>> Beatrice Kodero >>>>>>>> >>>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>>> more than anyone else." Vince Lombardi >>>>>>>> >>>>>>>> Mobile : +254 726 486 077 >>>>>>>> Skype : B.Kodero >>>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> Regards, >>>>>> Beatrice Kodero >>>>>> >>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>> more than anyone else." Vince Lombardi >>>>>> >>>>>> Mobile : +254 726 486 077 >>>>>> Skype : B.Kodero >>>>>> >>>>> >>>> >>>> -- >>>> >>>> Regards, >>>> Beatrice Kodero >>>> >>>> "Winning means you're willing to go longer, work harder, and give more >>>> than anyone else." Vince Lombardi >>>> >>>> Mobile : +254 726 486 077 >>>> Skype : B.Kodero >>>> >>> >>> >>> -- >>> >>> Regards, >>> Beatrice Kodero >>> >>> "Winning means you're willing to go longer, work harder, and give more >>> than anyone else." Vince Lombardi >>> >>> Mobile : +254 726 486 077 >>> Skype : B.Kodero >>> >>> <WhatsApp Image 2018-10-23 at 8.28.07 PM(1).jpeg> >>> >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> >>> |
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From: Beatrice K. <kod...@gm...> - 2018-10-23 23:44:34
|
Please allow me to ask, After installation and I want to preload data to my localhost ie i don't have to upload a reference gene or add track something like this here <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> What files will i work with? jbrowse.conf or tracks.conf or hard code? Regards Beatrice On Tue, Oct 23, 2018, 9:40 PM Beatrice Kodero <kod...@gm...> wrote: > Hey Scott, > > It's blank > > On Tue, Oct 23, 2018, 9:06 PM Scott Cain <sc...@sc...> wrote: > >> Hi Beatrice, >> >> I can’t quite make out the text in the red bar (where the error message >> is). Can you tell us what it says? >> >> Thanks, Scott >> >> On Oct 23, 2018, at 10:31 AM, Beatrice Kodero <kod...@gm...> >> wrote: >> >> Please find attached. The error I am now getting from installation >> >> On Tue, Oct 23, 2018 at 8:21 PM Beatrice Kodero <kod...@gm...> >> wrote: >> >>> Garrett Thanks a million. >>> >>> Able to download at cd/var/www/html/jbrowse >>> >>> Please allow me to ask, After installation and I want to preload data to >>> my localhost ie i don't have to upload a reference gene or add track >>> something like this here >>> >>> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >>> What files will i work with? jbrowse.conf or tracks.conf or hard code. >>> >>> On Tue, Oct 23, 2018 at 7:47 PM Garrett Stevens < >>> ste...@gm...> wrote: >>> >>>> Either should work, as long as you specify the paths to the files >>>> correctly. E.g. >>>> >>>> cd /var/www/html/jbrowse >>>> bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz >>>> >>>> and >>>> >>>> cd /var/www/html/jbrowse/data >>>> bgzip volvox.sorted.gff3 tabix -p gff volvox.sorted.gff3.gz >>>> >>>> should both work. >>>> >>>> ~Garrett >>>> >>>> On Tue, Oct 23, 2018 at 12:00 PM Beatrice Kodero <kod...@gm...> >>>> wrote: >>>> >>>>> thanks for your mail again, >>>>> >>>>> kindly clarify should I be /var/www/html/jbrowse/data or >>>>> /var/www/html/jbrowse >>>>> >>>>> Been working from /var/www/html/jbrowse/data to install content of >>>>> https://jbrowse.org/docs/tutorial.html ie FASTA, GFF3 >>>>> >>>>> Thanks >>>>> >>>>> On Tue, Oct 23, 2018 at 6:50 PM Garrett Stevens < >>>>> ste...@gm...> wrote: >>>>> >>>>>> Ok, so looking at the error in your first message, it looks like you >>>>>> perhaps weren't in the right location when you ran the bgzip and tabix >>>>>> commands. Those are the commands that will generate the files you are >>>>>> missing. Try making sure you cd to the right directory first, like: >>>>>> >>>>>> cd /var/www/html/jbrowse >>>>>> bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz >>>>>> >>>>>> ~Garrett >>>>>> >>>>>> On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero <kod...@gm...> >>>>>> wrote: >>>>>> >>>>>>> Thanks for apt response Garrett >>>>>>> >>>>>>> I am following step step process on the link http://jbrowse.org/docs/installation.html >>>>>>> . >>>>>>> >>>>>>> <http://jbrowse.org/docs/installation.html> >>>>>>> I used wget and downloaded above. The challenge am facing begins at >>>>>>> http://jbrowse.org/docs/tutorial.html >>>>>>> >>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa >>>>>>> >>>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 >>>>>>> >>>>>>> I only got these files >>>>>>> tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 >>>>>>> >>>>>>> Instead of below files >>>>>>> /var/www/html/jbrowse >>>>>>> /var/www/html/jbrowse/data >>>>>>> /var/www/html/jbrowse/data/volvox.fa >>>>>>> /var/www/html/jbrowse/data/volvox.fa.fai >>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz >>>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi >>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam >>>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam.bai >>>>>>> /var/www/html/jbrowse/data/tracks.conf >>>>>>> >>>>>>> I am missing >>>>>>> >>>>>>> volvox.sorted.gff3.gz >>>>>>> >>>>>>> volvox.sorted.gff3.gz.tbi >>>>>>> >>>>>>> Kindly advise. >>>>>>> >>>>>>> Regards >>>>>>> >>>>>>> Beatrice >>>>>>> >>>>>>> >>>>>>> On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens < >>>>>>> ste...@gm...> wrote: >>>>>>> >>>>>>>> Hello, >>>>>>>> >>>>>>>> When you say the curl link is not working, what do you mean? Are >>>>>>>> you using the installation instructions found here >>>>>>>> <http://jbrowse.org/docs/installation.html>? I tried the curl >>>>>>>> command on that page and it worked fine for me: >>>>>>>> >>>>>>>> curl -O >>>>>>>> https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >>>>>>>> >>>>>>>> Also the output you pasted was something with bgzip, not curl, so >>>>>>>> I'm not sure what the problem is there. If you can give some more detail we >>>>>>>> can see if we can help. >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Garrett >>>>>>>> >>>>>>>> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero < >>>>>>>> kod...@gm...> wrote: >>>>>>>> >>>>>>>>> Hi , >>>>>>>>> >>>>>>>>> I trust that this email finds you well. >>>>>>>>> >>>>>>>>> I am at the point of installing jbowse and the curl link is not >>>>>>>>> working. see below installation >>>>>>>>> >>>>>>>>> bgzip data/volvox.sorted.gff3 >>>>>>>>> >>>>>>>>> [bgzip] No such file or directory: data/volvox.sorted.gff3...........error >>>>>>>>> am getting. >>>>>>>>> >>>>>>>>> What could i be doing wrong? >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> Regards, >>>>>>>>> Beatrice Kodero >>>>>>>>> >>>>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>>>> more than anyone else." Vince Lombardi >>>>>>>>> >>>>>>>>> Mobile : +254 726 486 077 >>>>>>>>> Skype : B.Kodero >>>>>>>>> _______________________________________________ >>>>>>>>> Gmod-ajax mailing list >>>>>>>>> Gmo...@li... >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> Regards, >>>>>>> Beatrice Kodero >>>>>>> >>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>> more than anyone else." Vince Lombardi >>>>>>> >>>>>>> Mobile : +254 726 486 077 >>>>>>> Skype : B.Kodero >>>>>>> >>>>>> >>>>> >>>>> -- >>>>> >>>>> Regards, >>>>> Beatrice Kodero >>>>> >>>>> "Winning means you're willing to go longer, work harder, and give more >>>>> than anyone else." Vince Lombardi >>>>> >>>>> Mobile : +254 726 486 077 >>>>> Skype : B.Kodero >>>>> >>>> >>> >>> -- >>> >>> Regards, >>> Beatrice Kodero >>> >>> "Winning means you're willing to go longer, work harder, and give more >>> than anyone else." Vince Lombardi >>> >>> Mobile : +254 726 486 077 >>> Skype : B.Kodero >>> >> >> >> -- >> >> Regards, >> Beatrice Kodero >> >> "Winning means you're willing to go longer, work harder, and give more >> than anyone else." Vince Lombardi >> >> Mobile : +254 726 486 077 >> Skype : B.Kodero >> >> <WhatsApp Image 2018-10-23 at 8.28.07 PM(1).jpeg> >> >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> >> |
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From: Beatrice K. <kod...@gm...> - 2018-10-23 18:41:21
|
Hey Scott, It's blank On Tue, Oct 23, 2018, 9:06 PM Scott Cain <sc...@sc...> wrote: > Hi Beatrice, > > I can’t quite make out the text in the red bar (where the error message > is). Can you tell us what it says? > > Thanks, Scott > > On Oct 23, 2018, at 10:31 AM, Beatrice Kodero <kod...@gm...> wrote: > > Please find attached. The error I am now getting from installation > > On Tue, Oct 23, 2018 at 8:21 PM Beatrice Kodero <kod...@gm...> > wrote: > >> Garrett Thanks a million. >> >> Able to download at cd/var/www/html/jbrowse >> >> Please allow me to ask, After installation and I want to preload data to >> my localhost ie i don't have to upload a reference gene or add track >> something like this here >> >> <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> >> What files will i work with? jbrowse.conf or tracks.conf or hard code. >> >> On Tue, Oct 23, 2018 at 7:47 PM Garrett Stevens < >> ste...@gm...> wrote: >> >>> Either should work, as long as you specify the paths to the files >>> correctly. E.g. >>> >>> cd /var/www/html/jbrowse >>> bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz >>> >>> and >>> >>> cd /var/www/html/jbrowse/data >>> bgzip volvox.sorted.gff3 tabix -p gff volvox.sorted.gff3.gz >>> >>> should both work. >>> >>> ~Garrett >>> >>> On Tue, Oct 23, 2018 at 12:00 PM Beatrice Kodero <kod...@gm...> >>> wrote: >>> >>>> thanks for your mail again, >>>> >>>> kindly clarify should I be /var/www/html/jbrowse/data or >>>> /var/www/html/jbrowse >>>> >>>> Been working from /var/www/html/jbrowse/data to install content of >>>> https://jbrowse.org/docs/tutorial.html ie FASTA, GFF3 >>>> >>>> Thanks >>>> >>>> On Tue, Oct 23, 2018 at 6:50 PM Garrett Stevens < >>>> ste...@gm...> wrote: >>>> >>>>> Ok, so looking at the error in your first message, it looks like you >>>>> perhaps weren't in the right location when you ran the bgzip and tabix >>>>> commands. Those are the commands that will generate the files you are >>>>> missing. Try making sure you cd to the right directory first, like: >>>>> >>>>> cd /var/www/html/jbrowse >>>>> bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz >>>>> >>>>> ~Garrett >>>>> >>>>> On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero <kod...@gm...> >>>>> wrote: >>>>> >>>>>> Thanks for apt response Garrett >>>>>> >>>>>> I am following step step process on the link http://jbrowse.org/docs/installation.html >>>>>> . >>>>>> >>>>>> <http://jbrowse.org/docs/installation.html> >>>>>> I used wget and downloaded above. The challenge am facing begins at >>>>>> http://jbrowse.org/docs/tutorial.html >>>>>> >>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa >>>>>> >>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 >>>>>> >>>>>> I only got these files >>>>>> tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 >>>>>> >>>>>> Instead of below files >>>>>> /var/www/html/jbrowse >>>>>> /var/www/html/jbrowse/data >>>>>> /var/www/html/jbrowse/data/volvox.fa >>>>>> /var/www/html/jbrowse/data/volvox.fa.fai >>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz >>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi >>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam >>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam.bai >>>>>> /var/www/html/jbrowse/data/tracks.conf >>>>>> >>>>>> I am missing >>>>>> >>>>>> volvox.sorted.gff3.gz >>>>>> >>>>>> volvox.sorted.gff3.gz.tbi >>>>>> >>>>>> Kindly advise. >>>>>> >>>>>> Regards >>>>>> >>>>>> Beatrice >>>>>> >>>>>> >>>>>> On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens < >>>>>> ste...@gm...> wrote: >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> When you say the curl link is not working, what do you mean? Are you >>>>>>> using the installation instructions found here >>>>>>> <http://jbrowse.org/docs/installation.html>? I tried the curl >>>>>>> command on that page and it worked fine for me: >>>>>>> >>>>>>> curl -O >>>>>>> https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >>>>>>> >>>>>>> Also the output you pasted was something with bgzip, not curl, so >>>>>>> I'm not sure what the problem is there. If you can give some more detail we >>>>>>> can see if we can help. >>>>>>> >>>>>>> Thanks, >>>>>>> Garrett >>>>>>> >>>>>>> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero < >>>>>>> kod...@gm...> wrote: >>>>>>> >>>>>>>> Hi , >>>>>>>> >>>>>>>> I trust that this email finds you well. >>>>>>>> >>>>>>>> I am at the point of installing jbowse and the curl link is not >>>>>>>> working. see below installation >>>>>>>> >>>>>>>> bgzip data/volvox.sorted.gff3 >>>>>>>> >>>>>>>> [bgzip] No such file or directory: data/volvox.sorted.gff3...........error >>>>>>>> am getting. >>>>>>>> >>>>>>>> What could i be doing wrong? >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> Regards, >>>>>>>> Beatrice Kodero >>>>>>>> >>>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>>> more than anyone else." Vince Lombardi >>>>>>>> >>>>>>>> Mobile : +254 726 486 077 >>>>>>>> Skype : B.Kodero >>>>>>>> _______________________________________________ >>>>>>>> Gmod-ajax mailing list >>>>>>>> Gmo...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> Regards, >>>>>> Beatrice Kodero >>>>>> >>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>> more than anyone else." Vince Lombardi >>>>>> >>>>>> Mobile : +254 726 486 077 >>>>>> Skype : B.Kodero >>>>>> >>>>> >>>> >>>> -- >>>> >>>> Regards, >>>> Beatrice Kodero >>>> >>>> "Winning means you're willing to go longer, work harder, and give more >>>> than anyone else." Vince Lombardi >>>> >>>> Mobile : +254 726 486 077 >>>> Skype : B.Kodero >>>> >>> >> >> -- >> >> Regards, >> Beatrice Kodero >> >> "Winning means you're willing to go longer, work harder, and give more >> than anyone else." Vince Lombardi >> >> Mobile : +254 726 486 077 >> Skype : B.Kodero >> > > > -- > > Regards, > Beatrice Kodero > > "Winning means you're willing to go longer, work harder, and give more > than anyone else." Vince Lombardi > > Mobile : +254 726 486 077 > Skype : B.Kodero > > <WhatsApp Image 2018-10-23 at 8.28.07 PM(1).jpeg> > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > |
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From: Scott C. <sc...@sc...> - 2018-10-23 18:35:25
|
Hi Beatrice, I can’t quite make out the text in the red bar (where the error message is). Can you tell us what it says? Thanks, Scott > On Oct 23, 2018, at 10:31 AM, Beatrice Kodero <kod...@gm...> wrote: > > Please find attached. The error I am now getting from installation > >> On Tue, Oct 23, 2018 at 8:21 PM Beatrice Kodero <kod...@gm...> wrote: >> Garrett Thanks a million. >> >> Able to download at cd/var/www/html/jbrowse >> >> Please allow me to ask, After installation and I want to preload data to my localhost ie i don't have to upload a reference gene or add track something like this here >> What files will i work with? jbrowse.conf or tracks.conf or hard code. >> >>> On Tue, Oct 23, 2018 at 7:47 PM Garrett Stevens <ste...@gm...> wrote: >>> Either should work, as long as you specify the paths to the files correctly. E.g. >>> >>> cd /var/www/html/jbrowse >>> bgzip data/volvox.sorted.gff3 >>> tabix -p gff data/volvox.sorted.gff3.gz >>> >>> and >>> >>> cd /var/www/html/jbrowse/data >>> bgzip volvox.sorted.gff3 >>> tabix -p gff volvox.sorted.gff3.gz >>> >>> should both work. >>> >>> ~Garrett >>> >>>> On Tue, Oct 23, 2018 at 12:00 PM Beatrice Kodero <kod...@gm...> wrote: >>>> thanks for your mail again, >>>> >>>> kindly clarify should I be /var/www/html/jbrowse/data or /var/www/html/jbrowse >>>> >>>> Been working from /var/www/html/jbrowse/data to install content of https://jbrowse.org/docs/tutorial.html ie FASTA, GFF3 >>>> >>>> Thanks >>>> >>>>> On Tue, Oct 23, 2018 at 6:50 PM Garrett Stevens <ste...@gm...> wrote: >>>>> Ok, so looking at the error in your first message, it looks like you perhaps weren't in the right location when you ran the bgzip and tabix commands. Those are the commands that will generate the files you are missing. Try making sure you cd to the right directory first, like: >>>>> >>>>> cd /var/www/html/jbrowse >>>>> bgzip data/volvox.sorted.gff3 >>>>> tabix -p gff data/volvox.sorted.gff3.gz >>>>> >>>>> ~Garrett >>>>> >>>>>> On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero <kod...@gm...> wrote: >>>>>> Thanks for apt response Garrett >>>>>> >>>>>> I am following step step process on the link http://jbrowse.org/docs/installation.html . >>>>>> >>>>>> I used wget and downloaded above. The challenge am facing begins at http://jbrowse.org/docs/tutorial.html >>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa >>>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 >>>>>> >>>>>> I only got these files >>>>>> tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 >>>>>> >>>>>> Instead of below files >>>>>> /var/www/html/jbrowse >>>>>> /var/www/html/jbrowse/data >>>>>> /var/www/html/jbrowse/data/volvox.fa >>>>>> /var/www/html/jbrowse/data/volvox.fa.fai >>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz >>>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi >>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam >>>>>> /var/www/html/jbrowse/data/volvox-sorted.bam.bai >>>>>> /var/www/html/jbrowse/data/tracks.conf >>>>>> >>>>>> I am missing >>>>>> volvox.sorted.gff3.gz >>>>>> volvox.sorted.gff3.gz.tbi >>>>>> >>>>>> Kindly advise. >>>>>> >>>>>> Regards >>>>>> Beatrice >>>>>> >>>>>>> On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens <ste...@gm...> wrote: >>>>>>> Hello, >>>>>>> >>>>>>> When you say the curl link is not working, what do you mean? Are you using the installation instructions found here? I tried the curl command on that page and it worked fine for me: >>>>>>> >>>>>>> curl -O https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >>>>>>> >>>>>>> Also the output you pasted was something with bgzip, not curl, so I'm not sure what the problem is there. If you can give some more detail we can see if we can help. >>>>>>> >>>>>>> Thanks, >>>>>>> Garrett >>>>>>> >>>>>>>> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero <kod...@gm...> wrote: >>>>>>>> Hi , >>>>>>>> >>>>>>>> I trust that this email finds you well. >>>>>>>> >>>>>>>> I am at the point of installing jbowse and the curl link is not working. see below installation >>>>>>>> >>>>>>>> bgzip data/volvox.sorted.gff3 >>>>>>>> >>>>>>>> [bgzip] No such file or directory: data/volvox.sorted.gff3...........error am getting. >>>>>>>> >>>>>>>> What could i be doing wrong? >>>>>>>> >>>>>>>> -- >>>>>>>> >>>>>>>> Regards, >>>>>>>> Beatrice Kodero >>>>>>>> >>>>>>>> "Winning means you're willing to go longer, work harder, and give more than anyone else." Vince Lombardi >>>>>>>> >>>>>>>> Mobile : +254 726 486 077 >>>>>>>> Skype : B.Kodero >>>>>>>> _______________________________________________ >>>>>>>> Gmod-ajax mailing list >>>>>>>> Gmo...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> Regards, >>>>>> Beatrice Kodero >>>>>> >>>>>> "Winning means you're willing to go longer, work harder, and give more than anyone else." Vince Lombardi >>>>>> >>>>>> Mobile : +254 726 486 077 >>>>>> Skype : B.Kodero >>>> >>>> >>>> -- >>>> >>>> Regards, >>>> Beatrice Kodero >>>> >>>> "Winning means you're willing to go longer, work harder, and give more than anyone else." Vince Lombardi >>>> >>>> Mobile : +254 726 486 077 >>>> Skype : B.Kodero >> >> >> -- >> >> Regards, >> Beatrice Kodero >> >> "Winning means you're willing to go longer, work harder, and give more than anyone else." Vince Lombardi >> >> Mobile : +254 726 486 077 >> Skype : B.Kodero > > > -- > > Regards, > Beatrice Kodero > > "Winning means you're willing to go longer, work harder, and give more than anyone else." Vince Lombardi > > Mobile : +254 726 486 077 > Skype : B.Kodero > <WhatsApp Image 2018-10-23 at 8.28.07 PM(1).jpeg> > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Beatrice K. <kod...@gm...> - 2018-10-23 17:32:10
|
Please find attached. The error I am now getting from installation On Tue, Oct 23, 2018 at 8:21 PM Beatrice Kodero <kod...@gm...> wrote: > Garrett Thanks a million. > > Able to download at cd/var/www/html/jbrowse > > Please allow me to ask, After installation and I want to preload data to > my localhost ie i don't have to upload a reference gene or add track > something like this here > > <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> > What files will i work with? jbrowse.conf or tracks.conf or hard code. > > On Tue, Oct 23, 2018 at 7:47 PM Garrett Stevens < > ste...@gm...> wrote: > >> Either should work, as long as you specify the paths to the files >> correctly. E.g. >> >> cd /var/www/html/jbrowse >> bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz >> >> and >> >> cd /var/www/html/jbrowse/data >> bgzip volvox.sorted.gff3 tabix -p gff volvox.sorted.gff3.gz >> >> should both work. >> >> ~Garrett >> >> On Tue, Oct 23, 2018 at 12:00 PM Beatrice Kodero <kod...@gm...> >> wrote: >> >>> thanks for your mail again, >>> >>> kindly clarify should I be /var/www/html/jbrowse/data or >>> /var/www/html/jbrowse >>> >>> Been working from /var/www/html/jbrowse/data to install content of >>> https://jbrowse.org/docs/tutorial.html ie FASTA, GFF3 >>> >>> Thanks >>> >>> On Tue, Oct 23, 2018 at 6:50 PM Garrett Stevens < >>> ste...@gm...> wrote: >>> >>>> Ok, so looking at the error in your first message, it looks like you >>>> perhaps weren't in the right location when you ran the bgzip and tabix >>>> commands. Those are the commands that will generate the files you are >>>> missing. Try making sure you cd to the right directory first, like: >>>> >>>> cd /var/www/html/jbrowse >>>> bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz >>>> >>>> ~Garrett >>>> >>>> On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero <kod...@gm...> >>>> wrote: >>>> >>>>> Thanks for apt response Garrett >>>>> >>>>> I am following step step process on the link http://jbrowse.org/docs/installation.html >>>>> . >>>>> >>>>> <http://jbrowse.org/docs/installation.html> >>>>> I used wget and downloaded above. The challenge am facing begins at >>>>> http://jbrowse.org/docs/tutorial.html >>>>> >>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa >>>>> >>>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 >>>>> >>>>> I only got these files >>>>> tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 >>>>> >>>>> Instead of below files >>>>> /var/www/html/jbrowse >>>>> /var/www/html/jbrowse/data >>>>> /var/www/html/jbrowse/data/volvox.fa >>>>> /var/www/html/jbrowse/data/volvox.fa.fai >>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz >>>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi >>>>> /var/www/html/jbrowse/data/volvox-sorted.bam >>>>> /var/www/html/jbrowse/data/volvox-sorted.bam.bai >>>>> /var/www/html/jbrowse/data/tracks.conf >>>>> >>>>> I am missing >>>>> >>>>> volvox.sorted.gff3.gz >>>>> >>>>> volvox.sorted.gff3.gz.tbi >>>>> >>>>> Kindly advise. >>>>> >>>>> Regards >>>>> >>>>> Beatrice >>>>> >>>>> >>>>> On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens < >>>>> ste...@gm...> wrote: >>>>> >>>>>> Hello, >>>>>> >>>>>> When you say the curl link is not working, what do you mean? Are you >>>>>> using the installation instructions found here >>>>>> <http://jbrowse.org/docs/installation.html>? I tried the curl >>>>>> command on that page and it worked fine for me: >>>>>> >>>>>> curl -O >>>>>> https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >>>>>> >>>>>> Also the output you pasted was something with bgzip, not curl, so I'm >>>>>> not sure what the problem is there. If you can give some more detail we can >>>>>> see if we can help. >>>>>> >>>>>> Thanks, >>>>>> Garrett >>>>>> >>>>>> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero <kod...@gm...> >>>>>> wrote: >>>>>> >>>>>>> Hi , >>>>>>> >>>>>>> I trust that this email finds you well. >>>>>>> >>>>>>> I am at the point of installing jbowse and the curl link is not >>>>>>> working. see below installation >>>>>>> >>>>>>> bgzip data/volvox.sorted.gff3 >>>>>>> >>>>>>> [bgzip] No such file or directory: data/volvox.sorted.gff3...........error >>>>>>> am getting. >>>>>>> >>>>>>> What could i be doing wrong? >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> Regards, >>>>>>> Beatrice Kodero >>>>>>> >>>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>>> more than anyone else." Vince Lombardi >>>>>>> >>>>>>> Mobile : +254 726 486 077 >>>>>>> Skype : B.Kodero >>>>>>> _______________________________________________ >>>>>>> Gmod-ajax mailing list >>>>>>> Gmo...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>>> >>>>>> >>>>> >>>>> -- >>>>> >>>>> Regards, >>>>> Beatrice Kodero >>>>> >>>>> "Winning means you're willing to go longer, work harder, and give more >>>>> than anyone else." Vince Lombardi >>>>> >>>>> Mobile : +254 726 486 077 >>>>> Skype : B.Kodero >>>>> >>>> >>> >>> -- >>> >>> Regards, >>> Beatrice Kodero >>> >>> "Winning means you're willing to go longer, work harder, and give more >>> than anyone else." Vince Lombardi >>> >>> Mobile : +254 726 486 077 >>> Skype : B.Kodero >>> >> > > -- > > Regards, > Beatrice Kodero > > "Winning means you're willing to go longer, work harder, and give more > than anyone else." Vince Lombardi > > Mobile : +254 726 486 077 > Skype : B.Kodero > -- Regards, Beatrice Kodero "Winning means you're willing to go longer, work harder, and give more than anyone else." Vince Lombardi Mobile : +254 726 486 077 Skype : B.Kodero |
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From: Beatrice K. <kod...@gm...> - 2018-10-23 17:21:24
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Garrett Thanks a million. Able to download at cd/var/www/html/jbrowse Please allow me to ask, After installation and I want to preload data to my localhost ie i don't have to upload a reference gene or add track something like this here <http://jbrowse.igs.umaryland.edu/t_parva/?loc=tp.assembly.567478335.1%3A196811..1774318&tracks=Muguga%20reference%20annotation&highlight=> What files will i work with? jbrowse.conf or tracks.conf or hard code. On Tue, Oct 23, 2018 at 7:47 PM Garrett Stevens <ste...@gm...> wrote: > Either should work, as long as you specify the paths to the files > correctly. E.g. > > cd /var/www/html/jbrowse > bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz > > and > > cd /var/www/html/jbrowse/data > bgzip volvox.sorted.gff3 tabix -p gff volvox.sorted.gff3.gz > > should both work. > > ~Garrett > > On Tue, Oct 23, 2018 at 12:00 PM Beatrice Kodero <kod...@gm...> > wrote: > >> thanks for your mail again, >> >> kindly clarify should I be /var/www/html/jbrowse/data or >> /var/www/html/jbrowse >> >> Been working from /var/www/html/jbrowse/data to install content of >> https://jbrowse.org/docs/tutorial.html ie FASTA, GFF3 >> >> Thanks >> >> On Tue, Oct 23, 2018 at 6:50 PM Garrett Stevens < >> ste...@gm...> wrote: >> >>> Ok, so looking at the error in your first message, it looks like you >>> perhaps weren't in the right location when you ran the bgzip and tabix >>> commands. Those are the commands that will generate the files you are >>> missing. Try making sure you cd to the right directory first, like: >>> >>> cd /var/www/html/jbrowse >>> bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz >>> >>> ~Garrett >>> >>> On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero <kod...@gm...> >>> wrote: >>> >>>> Thanks for apt response Garrett >>>> >>>> I am following step step process on the link http://jbrowse.org/docs/installation.html >>>> . >>>> >>>> <http://jbrowse.org/docs/installation.html> >>>> I used wget and downloaded above. The challenge am facing begins at >>>> http://jbrowse.org/docs/tutorial.html >>>> >>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa >>>> >>>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 >>>> >>>> I only got these files >>>> tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 >>>> >>>> Instead of below files >>>> /var/www/html/jbrowse >>>> /var/www/html/jbrowse/data >>>> /var/www/html/jbrowse/data/volvox.fa >>>> /var/www/html/jbrowse/data/volvox.fa.fai >>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz >>>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi >>>> /var/www/html/jbrowse/data/volvox-sorted.bam >>>> /var/www/html/jbrowse/data/volvox-sorted.bam.bai >>>> /var/www/html/jbrowse/data/tracks.conf >>>> >>>> I am missing >>>> >>>> volvox.sorted.gff3.gz >>>> >>>> volvox.sorted.gff3.gz.tbi >>>> >>>> Kindly advise. >>>> >>>> Regards >>>> >>>> Beatrice >>>> >>>> >>>> On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens < >>>> ste...@gm...> wrote: >>>> >>>>> Hello, >>>>> >>>>> When you say the curl link is not working, what do you mean? Are you >>>>> using the installation instructions found here >>>>> <http://jbrowse.org/docs/installation.html>? I tried the curl command >>>>> on that page and it worked fine for me: >>>>> >>>>> curl -O >>>>> https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >>>>> >>>>> Also the output you pasted was something with bgzip, not curl, so I'm >>>>> not sure what the problem is there. If you can give some more detail we can >>>>> see if we can help. >>>>> >>>>> Thanks, >>>>> Garrett >>>>> >>>>> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero <kod...@gm...> >>>>> wrote: >>>>> >>>>>> Hi , >>>>>> >>>>>> I trust that this email finds you well. >>>>>> >>>>>> I am at the point of installing jbowse and the curl link is not >>>>>> working. see below installation >>>>>> >>>>>> bgzip data/volvox.sorted.gff3 >>>>>> >>>>>> [bgzip] No such file or directory: data/volvox.sorted.gff3...........error >>>>>> am getting. >>>>>> >>>>>> What could i be doing wrong? >>>>>> >>>>>> -- >>>>>> >>>>>> Regards, >>>>>> Beatrice Kodero >>>>>> >>>>>> "Winning means you're willing to go longer, work harder, and give >>>>>> more than anyone else." Vince Lombardi >>>>>> >>>>>> Mobile : +254 726 486 077 >>>>>> Skype : B.Kodero >>>>>> _______________________________________________ >>>>>> Gmod-ajax mailing list >>>>>> Gmo...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>> >>>>> >>>> >>>> -- >>>> >>>> Regards, >>>> Beatrice Kodero >>>> >>>> "Winning means you're willing to go longer, work harder, and give more >>>> than anyone else." Vince Lombardi >>>> >>>> Mobile : +254 726 486 077 >>>> Skype : B.Kodero >>>> >>> >> >> -- >> >> Regards, >> Beatrice Kodero >> >> "Winning means you're willing to go longer, work harder, and give more >> than anyone else." Vince Lombardi >> >> Mobile : +254 726 486 077 >> Skype : B.Kodero >> > -- Regards, Beatrice Kodero "Winning means you're willing to go longer, work harder, and give more than anyone else." Vince Lombardi Mobile : +254 726 486 077 Skype : B.Kodero |
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From: Garrett S. <ste...@gm...> - 2018-10-23 16:47:28
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Either should work, as long as you specify the paths to the files correctly. E.g. cd /var/www/html/jbrowse bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz and cd /var/www/html/jbrowse/data bgzip volvox.sorted.gff3 tabix -p gff volvox.sorted.gff3.gz should both work. ~Garrett On Tue, Oct 23, 2018 at 12:00 PM Beatrice Kodero <kod...@gm...> wrote: > thanks for your mail again, > > kindly clarify should I be /var/www/html/jbrowse/data or > /var/www/html/jbrowse > > Been working from /var/www/html/jbrowse/data to install content of > https://jbrowse.org/docs/tutorial.html ie FASTA, GFF3 > > Thanks > > On Tue, Oct 23, 2018 at 6:50 PM Garrett Stevens < > ste...@gm...> wrote: > >> Ok, so looking at the error in your first message, it looks like you >> perhaps weren't in the right location when you ran the bgzip and tabix >> commands. Those are the commands that will generate the files you are >> missing. Try making sure you cd to the right directory first, like: >> >> cd /var/www/html/jbrowse >> bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz >> >> ~Garrett >> >> On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero <kod...@gm...> >> wrote: >> >>> Thanks for apt response Garrett >>> >>> I am following step step process on the link http://jbrowse.org/docs/installation.html >>> . >>> >>> <http://jbrowse.org/docs/installation.html> >>> I used wget and downloaded above. The challenge am facing begins at >>> http://jbrowse.org/docs/tutorial.html >>> >>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa >>> >>> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 >>> >>> I only got these files >>> tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 >>> >>> Instead of below files >>> /var/www/html/jbrowse >>> /var/www/html/jbrowse/data >>> /var/www/html/jbrowse/data/volvox.fa >>> /var/www/html/jbrowse/data/volvox.fa.fai >>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz >>> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi >>> /var/www/html/jbrowse/data/volvox-sorted.bam >>> /var/www/html/jbrowse/data/volvox-sorted.bam.bai >>> /var/www/html/jbrowse/data/tracks.conf >>> >>> I am missing >>> >>> volvox.sorted.gff3.gz >>> >>> volvox.sorted.gff3.gz.tbi >>> >>> Kindly advise. >>> >>> Regards >>> >>> Beatrice >>> >>> >>> On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens < >>> ste...@gm...> wrote: >>> >>>> Hello, >>>> >>>> When you say the curl link is not working, what do you mean? Are you >>>> using the installation instructions found here >>>> <http://jbrowse.org/docs/installation.html>? I tried the curl command >>>> on that page and it worked fine for me: >>>> >>>> curl -O >>>> https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >>>> >>>> Also the output you pasted was something with bgzip, not curl, so I'm >>>> not sure what the problem is there. If you can give some more detail we can >>>> see if we can help. >>>> >>>> Thanks, >>>> Garrett >>>> >>>> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero <kod...@gm...> >>>> wrote: >>>> >>>>> Hi , >>>>> >>>>> I trust that this email finds you well. >>>>> >>>>> I am at the point of installing jbowse and the curl link is not >>>>> working. see below installation >>>>> >>>>> bgzip data/volvox.sorted.gff3 >>>>> >>>>> [bgzip] No such file or directory: data/volvox.sorted.gff3...........error >>>>> am getting. >>>>> >>>>> What could i be doing wrong? >>>>> >>>>> -- >>>>> >>>>> Regards, >>>>> Beatrice Kodero >>>>> >>>>> "Winning means you're willing to go longer, work harder, and give more >>>>> than anyone else." Vince Lombardi >>>>> >>>>> Mobile : +254 726 486 077 >>>>> Skype : B.Kodero >>>>> _______________________________________________ >>>>> Gmod-ajax mailing list >>>>> Gmo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>> >>>> >>> >>> -- >>> >>> Regards, >>> Beatrice Kodero >>> >>> "Winning means you're willing to go longer, work harder, and give more >>> than anyone else." Vince Lombardi >>> >>> Mobile : +254 726 486 077 >>> Skype : B.Kodero >>> >> > > -- > > Regards, > Beatrice Kodero > > "Winning means you're willing to go longer, work harder, and give more > than anyone else." Vince Lombardi > > Mobile : +254 726 486 077 > Skype : B.Kodero > |
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From: Beatrice K. <kod...@gm...> - 2018-10-23 16:00:49
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thanks for your mail again, kindly clarify should I be /var/www/html/jbrowse/data or /var/www/html/jbrowse Been working from /var/www/html/jbrowse/data to install content of https://jbrowse.org/docs/tutorial.html ie FASTA, GFF3 Thanks On Tue, Oct 23, 2018 at 6:50 PM Garrett Stevens <ste...@gm...> wrote: > Ok, so looking at the error in your first message, it looks like you > perhaps weren't in the right location when you ran the bgzip and tabix > commands. Those are the commands that will generate the files you are > missing. Try making sure you cd to the right directory first, like: > > cd /var/www/html/jbrowse > bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz > > ~Garrett > > On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero <kod...@gm...> > wrote: > >> Thanks for apt response Garrett >> >> I am following step step process on the link http://jbrowse.org/docs/installation.html >> . >> >> <http://jbrowse.org/docs/installation.html> >> I used wget and downloaded above. The challenge am facing begins at >> http://jbrowse.org/docs/tutorial.html >> >> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa >> >> curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 >> >> I only got these files >> tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 >> >> Instead of below files >> /var/www/html/jbrowse >> /var/www/html/jbrowse/data >> /var/www/html/jbrowse/data/volvox.fa >> /var/www/html/jbrowse/data/volvox.fa.fai >> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz >> /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi >> /var/www/html/jbrowse/data/volvox-sorted.bam >> /var/www/html/jbrowse/data/volvox-sorted.bam.bai >> /var/www/html/jbrowse/data/tracks.conf >> >> I am missing >> >> volvox.sorted.gff3.gz >> >> volvox.sorted.gff3.gz.tbi >> >> Kindly advise. >> >> Regards >> >> Beatrice >> >> >> On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens < >> ste...@gm...> wrote: >> >>> Hello, >>> >>> When you say the curl link is not working, what do you mean? Are you >>> using the installation instructions found here >>> <http://jbrowse.org/docs/installation.html>? I tried the curl command >>> on that page and it worked fine for me: >>> >>> curl -O >>> https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >>> >>> Also the output you pasted was something with bgzip, not curl, so I'm >>> not sure what the problem is there. If you can give some more detail we can >>> see if we can help. >>> >>> Thanks, >>> Garrett >>> >>> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero <kod...@gm...> >>> wrote: >>> >>>> Hi , >>>> >>>> I trust that this email finds you well. >>>> >>>> I am at the point of installing jbowse and the curl link is not >>>> working. see below installation >>>> >>>> bgzip data/volvox.sorted.gff3 >>>> >>>> [bgzip] No such file or directory: data/volvox.sorted.gff3...........error >>>> am getting. >>>> >>>> What could i be doing wrong? >>>> >>>> -- >>>> >>>> Regards, >>>> Beatrice Kodero >>>> >>>> "Winning means you're willing to go longer, work harder, and give more >>>> than anyone else." Vince Lombardi >>>> >>>> Mobile : +254 726 486 077 >>>> Skype : B.Kodero >>>> _______________________________________________ >>>> Gmod-ajax mailing list >>>> Gmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>> >>> >> >> -- >> >> Regards, >> Beatrice Kodero >> >> "Winning means you're willing to go longer, work harder, and give more >> than anyone else." Vince Lombardi >> >> Mobile : +254 726 486 077 >> Skype : B.Kodero >> > -- Regards, Beatrice Kodero "Winning means you're willing to go longer, work harder, and give more than anyone else." Vince Lombardi Mobile : +254 726 486 077 Skype : B.Kodero |
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From: Garrett S. <ste...@gm...> - 2018-10-23 15:50:14
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Ok, so looking at the error in your first message, it looks like you perhaps weren't in the right location when you ran the bgzip and tabix commands. Those are the commands that will generate the files you are missing. Try making sure you cd to the right directory first, like: cd /var/www/html/jbrowse bgzip data/volvox.sorted.gff3 tabix -p gff data/volvox.sorted.gff3.gz ~Garrett On Tue, Oct 23, 2018 at 11:36 AM Beatrice Kodero <kod...@gm...> wrote: > Thanks for apt response Garrett > > I am following step step process on the link http://jbrowse.org/docs/installation.html > . > > <http://jbrowse.org/docs/installation.html> > I used wget and downloaded above. The challenge am facing begins at > http://jbrowse.org/docs/tutorial.html > > curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa > > curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 > > I only got these files > tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 > > Instead of below files > /var/www/html/jbrowse > /var/www/html/jbrowse/data > /var/www/html/jbrowse/data/volvox.fa > /var/www/html/jbrowse/data/volvox.fa.fai > /var/www/html/jbrowse/data/volvox.sorted.gff3.gz > /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi > /var/www/html/jbrowse/data/volvox-sorted.bam > /var/www/html/jbrowse/data/volvox-sorted.bam.bai > /var/www/html/jbrowse/data/tracks.conf > > I am missing > > volvox.sorted.gff3.gz > > volvox.sorted.gff3.gz.tbi > > Kindly advise. > > Regards > > Beatrice > > > On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens < > ste...@gm...> wrote: > >> Hello, >> >> When you say the curl link is not working, what do you mean? Are you >> using the installation instructions found here >> <http://jbrowse.org/docs/installation.html>? I tried the curl command on >> that page and it worked fine for me: >> >> curl -O >> https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip >> >> Also the output you pasted was something with bgzip, not curl, so I'm not >> sure what the problem is there. If you can give some more detail we can see >> if we can help. >> >> Thanks, >> Garrett >> >> On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero <kod...@gm...> >> wrote: >> >>> Hi , >>> >>> I trust that this email finds you well. >>> >>> I am at the point of installing jbowse and the curl link is not working. >>> see below installation >>> >>> bgzip data/volvox.sorted.gff3 >>> >>> [bgzip] No such file or directory: data/volvox.sorted.gff3...........error >>> am getting. >>> >>> What could i be doing wrong? >>> >>> -- >>> >>> Regards, >>> Beatrice Kodero >>> >>> "Winning means you're willing to go longer, work harder, and give more >>> than anyone else." Vince Lombardi >>> >>> Mobile : +254 726 486 077 >>> Skype : B.Kodero >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> >> > > -- > > Regards, > Beatrice Kodero > > "Winning means you're willing to go longer, work harder, and give more > than anyone else." Vince Lombardi > > Mobile : +254 726 486 077 > Skype : B.Kodero > |
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From: Beatrice K. <kod...@gm...> - 2018-10-23 15:36:12
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Thanks for apt response Garrett I am following step step process on the link http://jbrowse.org/docs/installation.html . <http://jbrowse.org/docs/installation.html> I used wget and downloaded above. The challenge am facing begins at http://jbrowse.org/docs/tutorial.html curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.fa > data/volvox.fa curl -L http://jbrowse.org/code/latest-release/docs/tutorial/data_files/volvox.gff3 > data/volvox.gff3 I only got these files tracklist.json trackList.json tracks.conf volvox.fa volvox.gff3 volvox-sorted.bam volvox.sorted.gff3 Instead of below files /var/www/html/jbrowse /var/www/html/jbrowse/data /var/www/html/jbrowse/data/volvox.fa /var/www/html/jbrowse/data/volvox.fa.fai /var/www/html/jbrowse/data/volvox.sorted.gff3.gz /var/www/html/jbrowse/data/volvox.sorted.gff3.gz.tbi /var/www/html/jbrowse/data/volvox-sorted.bam /var/www/html/jbrowse/data/volvox-sorted.bam.bai /var/www/html/jbrowse/data/tracks.conf I am missing volvox.sorted.gff3.gz volvox.sorted.gff3.gz.tbi Kindly advise. Regards Beatrice On Tue, Oct 23, 2018 at 6:18 PM Garrett Stevens <ste...@gm...> wrote: > Hello, > > When you say the curl link is not working, what do you mean? Are you using > the installation instructions found here > <http://jbrowse.org/docs/installation.html>? I tried the curl command on > that page and it worked fine for me: > > curl -O > https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip > > Also the output you pasted was something with bgzip, not curl, so I'm not > sure what the problem is there. If you can give some more detail we can see > if we can help. > > Thanks, > Garrett > > On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero <kod...@gm...> > wrote: > >> Hi , >> >> I trust that this email finds you well. >> >> I am at the point of installing jbowse and the curl link is not working. >> see below installation >> >> bgzip data/volvox.sorted.gff3 >> >> [bgzip] No such file or directory: data/volvox.sorted.gff3...........error >> am getting. >> >> What could i be doing wrong? >> >> -- >> >> Regards, >> Beatrice Kodero >> >> "Winning means you're willing to go longer, work harder, and give more >> than anyone else." Vince Lombardi >> >> Mobile : +254 726 486 077 >> Skype : B.Kodero >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > -- Regards, Beatrice Kodero "Winning means you're willing to go longer, work harder, and give more than anyone else." Vince Lombardi Mobile : +254 726 486 077 Skype : B.Kodero |
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From: Garrett S. <ste...@gm...> - 2018-10-23 15:18:23
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Hello, When you say the curl link is not working, what do you mean? Are you using the installation instructions found here <http://jbrowse.org/docs/installation.html>? I tried the curl command on that page and it worked fine for me: curl -O https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip Also the output you pasted was something with bgzip, not curl, so I'm not sure what the problem is there. If you can give some more detail we can see if we can help. Thanks, Garrett On Tue, Oct 23, 2018 at 11:13 AM Beatrice Kodero <kod...@gm...> wrote: > Hi , > > I trust that this email finds you well. > > I am at the point of installing jbowse and the curl link is not working. > see below installation > > bgzip data/volvox.sorted.gff3 > > [bgzip] No such file or directory: data/volvox.sorted.gff3...........error > am getting. > > What could i be doing wrong? > > -- > > Regards, > Beatrice Kodero > > "Winning means you're willing to go longer, work harder, and give more > than anyone else." Vince Lombardi > > Mobile : +254 726 486 077 > Skype : B.Kodero > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Beatrice K. <kod...@gm...> - 2018-10-23 11:54:19
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Hi , I trust that this email finds you well. I am at the point of installing jbowse and the curl link is not working. see below installation bgzip data/volvox.sorted.gff3 [bgzip] No such file or directory: data/volvox.sorted.gff3...........error am getting. What could i be doing wrong? -- Regards, Beatrice Kodero "Winning means you're willing to go longer, work harder, and give more than anyone else." Vince Lombardi Mobile : +254 726 486 077 Skype : B.Kodero |
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From: Scott C. <sc...@sc...> - 2018-10-18 19:14:56
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Hi All, It's that time of year again: if you would be interested in presenting in the GMOD workshop at PAG in San Diego this January, please let me know. You don't have to have a full blown abstract yet; a general idea of what you'd like to talk about is fine. If you know anybody who might be interested but isn't on one of these lists, please feel free to forward this to them. Thanks, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Nathan D. <nat...@lb...> - 2018-10-11 20:30:32
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Sorry, I mean JBrowse. Autocorrect is a bit agressive. Cross-posting to their list in case there is any additional info. > On Oct 11, 2018, at 1:11 PM, Nathan Dunn <nat...@lb...> wrote: > > > It is in the works AFAIK via Browse. > > Once implemented (months, years?), we should be able to take advantage of it. > > >> On Oct 11, 2018, at 12:53 PM, Michael Poeschla <Mic...@ag...> wrote: >> >> Hi, >> >> saw some stuff on nabble about work being done on a synteny tool for genome apollo. Has that been implemented, or is it in the works? >> >> Thanks, >> Michael >> >> >> >> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ >> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to sy...@li... | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. >> > |
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From: Colin <col...@gm...> - 2018-10-05 14:42:27
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Hello all, I'm pleased to announce that JBrowse 1.15.4 has been released! This release allows you to use bgzip indexed FASTA, adds a new categoryOrder config for sorting the Hierarchical track selector, and more! Thanks to everyone for their feature requests and bug reports, and enjoy! - JBrowse-1.15.4.zip <https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip> - minified release - JBrowse-1.15.4-dev.zip <https://github.com/GMOD/jbrowse/archive/1.15.4-release.zip> - use this if you modify jbrowse source code or use plugins - JBrowse-1.15.4-desktop-win32-x64.zip <https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4-desktop-win32-x64.zip> - JBrowse-1.15.4-desktop-linux-x64.zip <https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4-desktop-linux-x64.zip> - JBrowse-1.15.4-desktop-darwin-x64.zip <https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4-desktop-darwin-x64.zip> Blog post http://jbrowse.org/blog/2018/10/05/jbrowse-1-15-4.html <http://jbrowse.org/blog/#minor-improvements>Minor improvements - Added support for bgzipped indexed FASTA. To use, bgzip your FASTA with bgzip -i file.fa, which generates file.fa.gz and file.fa.gzi and then usesamtools faidx file.fa.gz. If you specify the .fa.gz in the track config e.g. "urlTemplate": "file.fa.gz" and have all three files in your data directory, then they will automatically be detected (issue #1152 <https://github.com/gmod/jbrowse/issues/1152>, issue #1200 <https://github.com/gmod/jbrowse/pull/1200>, @cmdcolin <https://github.com/cmdcolin>) - Allow fna and mfa file extensions for FASTA to be recognized by default in the Open sequence dialog (issue #1205 <https://github.com/gmod/jbrowse/issues/1205>, @cmdcolin <https://github.com/cmdcolin>) - Improve the layout slightly for dense features (issue #1210 <https://github.com/gmod/jbrowse/issues/1210>, @cmdcolin <https://github.com/cmdcolin>) - Added a topLevelFeaturesPercent configuration variable that can be used to correct feature statistics estimates when topLevelFeatures is being used for a track, or when it contains deeply-nested features. This configuration variable is currently only used by BAM, BEDTabix, GFF3Tabix, and VCFTabix stores. (issue #1147 <https://github.com/gmod/jbrowse/issues/1147>, issue #1209 <https://github.com/gmod/jbrowse/pull/1209>, @rbuels <https://github.com/rbuels>) - Tabix-based data stores use a new storage backend based on the @gmod/tabix npm module. Users should see some modest performance improvements for Tabix-based tracks. (issue #1195 <https://github.com/gmod/jbrowse/issues/1195>, issue #1209 <https://github.com/gmod/jbrowse/pull/1209>, @rbuels <https://github.com/rbuels>) - Added hideSequenceBox config to allow hiding the FASTA boxes in the View details popups. Thanks to @andreamini <https://github.com/andreamini> for reporting (issue #1211 <https://github.com/gmod/jbrowse/issues/1211>, issue #1219 <https://github.com/gmod/jbrowse/pull/1219>, @cmdcolin <https://github.com/cmdcolin>) - Added categoryOrder config to allow sorting the categories in the Hierarchical track selector. For example, categoryOrder=VCF,Quantitative/Density,BAM. Note that we specify a lowest level subcategory e.g. Quantitative/Density to sort the parent category Quantitative to a position (issue #1203 <https://github.com/gmod/jbrowse/issues/1203>, issue #1208 <https://github.com/gmod/jbrowse/pull/1208>, @cmdcolin <https://github.com/cmdcolin>) <http://jbrowse.org/blog/#bug-fixes>Bug fixes - Fixed a bug in which feature labels would sometimes be repeated across the view, in the wrong locations. (@rbuels <https://github.com/rbuels>) - Fixed error where a chunk size limit error during histogram display would not be displayed (@cmdcolin <https://github.com/cmdcolin>) - Fixed issue where Open sequence dialog will open up the default "data" directory instead of a blank instance (issue #1207 <https://github.com/gmod/jbrowse/issues/1207>, @cmdcolin <https://github.com/cmdcolin>) - Added check for PCR duplicates for CRAM features (@cmdcolin <https://github.com/cmdcolin>) - Fixed issue where editing the track names and types in the "Open track" dialog box was not working when editing multiple tracks (issue #1217 <https://github.com/gmod/jbrowse/issues/1217>, @cmdcolin <https://github.com/cmdcolin>) - Fixed issue in which large VCF headers were not always correctly parsed by JBrowse (issue #1139 <https://github.com/gmod/jbrowse/issues/1139>, issue #1209 <https://github.com/gmod/jbrowse/pull/1209>, @rbuels <https://github.com/rbuels>) - Fixed issue where the histogram Y-scale bar would appear over features (issue #1214, issue #1218 <https://github.com/gmod/jbrowse/pull/1218>, @cmdcolin <https://github.com/cmdcolin>) |
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