Recent changes to Home

Home modified by Houxiang Zhu

Houxiang Zhu — Tue, 22 Dec 2015 16:58:27 -0000

--- v72
+++ v73
@@ -58,8 +58,8 @@
           ./setup.sh**
        * Create a folder called “data” under /var/www/JBrowse/JBrowse-1.11.6 
        * Create a folder called “userData” under /var/www/JBrowse/JBrowse-1.11.6/data.
-       * ~~~ To add any new reference genome, repeat steps in this block. Change “TAIR10.27” in this block to the reference genome name (e.g. GRCh38.81) that you want to add ~~~
-       * To add a reference genome, also create a folder under /var/www/JBrowse/JBrowse-1.11.6/data. For example: create a folder called “TAIR10.27” under /var/www/JBrowse/JBrowse-1.11.6/data. Then create two folders - “genome” and “gff” - under the reference genome folder (/var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27).
+       * ~~~~~~~~~~~~~~~~ To add any new reference genome, repeat steps in this block. Change “TAIR10.27” in this block to the reference genome name (e.g. GRCh38.81) that you want to add ~~~~~~~~~~~~~~~~~
+       * To add a reference genome, create a folder under /var/www/JBrowse/JBrowse-1.11.6/data. For example: create a folder called “TAIR10.27” under /var/www/JBrowse/JBrowse-1.11.6/data. Then create two folders - “genome” and “gff” - under the reference genome folder (/var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27).
        * Download the TAIR10.27 genome (or any reference genome) from [Ensembl](ftp://ftp.ensemblgenomes.org/pub/plants/release-27/fasta/arabidopsis_thaliana/dna/). Download each chromosome separately, and then unzip them and put into the appropriate reference genome folder, e.g. /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome  (Note: only unzipped chromosome files should be put in the /www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome/ folder).
        * Concatenate the genome into a single FASTA file. Model your commands after the following example:
           **cd /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome
@@ -78,11 +78,12 @@
           sudo chmod o-w /var/www**

 Installing CT-Finder
-* TAIR10 will be used as the example reference genome in this manual. Change names of folders and files as appropriate for the reference genome you are using.
+* TAIR10.27 will be used as the example reference genome in this manual. Change names of folders and files as appropriate for the reference genome you are using.
 * Download [ct-finder.zip](https://sourceforge.net/projects/ct-finder/files/latest/download) and unzip it. Put it into the root directory of the apache server (e.g. /var/www/ on Debian or Ubuntu systems, /var/www/html on Red Hat, Fedora, or SUSE. /var/www/ is used as an example in this guide).
+* ~~~~~~~~~~~~~~~~ To add any new reference genome, repeat steps in this block. Change “TAIR10.27” in this block to the reference genome name (e.g. GRCh38.81) that you want to add. Note: the reference genome name here must be the same as above block part ~~~~~~~~~~~~~~~~~
 * Create a folder named according to the genome name that you want to add under /var/www/ct-finder/bowtie2db/. E.g. “TAIR10.27” under /var/www/ct-finder/bowtie2db/.
-* Copy the TAIR10 genome (TAIR10.27.fa) from /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome/ folder into /var/www/ct-finder/bowtie2db/TAIR10.27/ folder.
-* Create a .txt file called “TAIR10.27_chr.txt”, including TAIR10 chromosome names, in the /var/www/ct-finder/bowtie2db/TAIR10.27/ folder (Note: all chromosome names in “TAIR10.27_chr.txt” file must be the same as the names in "TAIR10.27.fa" file). Refer to the format in /var/www/ct-finder/example/TAIR10.27_chr.txt.
+* Copy the TAIR10.27 genome (TAIR10.27.fa) from /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome/ folder into /var/www/ct-finder/bowtie2db/TAIR10.27/ folder.
+* Create a .txt file called “TAIR10.27_chr.txt”, including TAIR10.27 chromosome names, in the /var/www/ct-finder/bowtie2db/TAIR10.27/ folder (Note: all chromosome names in “TAIR10.27_chr.txt” file must be the same as the names in "TAIR10.27.fa" file). Refer to the format in /var/www/ct-finder/example/TAIR10.27_chr.txt.
 * Build the bowtie2 index. This may take some time, depending on the size of the reference genome. Model your commands after the following examples:
    **cd /var/www/ct-finder/bowtie2db/TAIR10.27/
    bowtie2-build TAIR10.27.fa TAIR10.27**
@@ -91,6 +92,7 @@
    sudo chgrp www-data TAIR10.27
    sudo chmod g+rwx TAIR10.27**
 * Go to /var/www/ct-finder/interface folder to edit the files “Cas9.php”, “Cas9n.php” and “RFNs.php”. Open “Cas9.php”, and then add one line of code “<option value=TAIR10.27 >Ensembl Thale cress (Arabidopsis thaliana) genome TAIR10.27</option>” below “<option value=none>Choose an organism</option>” (Note: the "TAIR10.27" in "value=TAIR10.27" is the name of your reference genome folder). Do the same for “Cas9n.php” and “RFNs.php”.
+* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 * Go to /var/www/ct-finder/ folder to edit “root_path.php” file. Open it and Configure the following parameters to reflect the actual location paths in your setup:
        * JBROWSE_USERDATA_PATH: set the absolute path for folder “userData” in JBrowse.
        * JBROWSE_RELATIVE_PATH: set the relative path for folder “JBrowse-1.11.6” in JBrowse. Here it is relative to /var/www/ (the default apache root directory).

Home modified by Houxiang Zhu

Houxiang Zhu — Tue, 22 Dec 2015 16:44:03 -0000

--- v71
+++ v72
@@ -58,7 +58,7 @@
           ./setup.sh**
        * Create a folder called “data” under /var/www/JBrowse/JBrowse-1.11.6 
        * Create a folder called “userData” under /var/www/JBrowse/JBrowse-1.11.6/data.
-       * ### To add any new reference genome, repeat steps in this block. Change “TAIR10.27” in this block to the reference genome that you want to add ###
+       * ~~~ To add any new reference genome, repeat steps in this block. Change “TAIR10.27” in this block to the reference genome name (e.g. GRCh38.81) that you want to add ~~~
        * To add a reference genome, also create a folder under /var/www/JBrowse/JBrowse-1.11.6/data. For example: create a folder called “TAIR10.27” under /var/www/JBrowse/JBrowse-1.11.6/data. Then create two folders - “genome” and “gff” - under the reference genome folder (/var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27).
        * Download the TAIR10.27 genome (or any reference genome) from [Ensembl](ftp://ftp.ensemblgenomes.org/pub/plants/release-27/fasta/arabidopsis_thaliana/dna/). Download each chromosome separately, and then unzip them and put into the appropriate reference genome folder, e.g. /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome  (Note: only unzipped chromosome files should be put in the /www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome/ folder).
        * Concatenate the genome into a single FASTA file. Model your commands after the following example:
@@ -70,7 +70,7 @@
           ./bin/prepare-refseqs.pl --fasta data/TAIR10.27/genome/TAIR10.27.fa --out data/TAIR10.27/
           ./bin/flatfile-to-json.pl --gff data/TAIR10.27/gff/TAIR10.27.gff3 --type transcript --trackLabel transcript --out data/TAIR10.27**
        * Access http://localhost/JBrowse/JBrowse-1.11.6/?data=data/TAIR10.27 to check that you have sucessfully added TAIR10 genome to JBrowse 
-       * ######################################################################## 
+       * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
        * Enter the following commands into the command line:
          ** cd /var/www/JBrowse/JBrowse-1.11.6/data/
           sudo chgrp www-data userData/

Home modified by Houxiang Zhu

Houxiang Zhu — Tue, 22 Dec 2015 16:39:29 -0000

--- v70
+++ v71
@@ -58,7 +58,7 @@
           ./setup.sh**
        * Create a folder called “data” under /var/www/JBrowse/JBrowse-1.11.6 
        * Create a folder called “userData” under /var/www/JBrowse/JBrowse-1.11.6/data.
-       * ###To add any new reference genome, repeat steps in this block. Change “TAIR10.27” in this block to the reference genome that you want to add###
+       * ### To add any new reference genome, repeat steps in this block. Change “TAIR10.27” in this block to the reference genome that you want to add ###
        * To add a reference genome, also create a folder under /var/www/JBrowse/JBrowse-1.11.6/data. For example: create a folder called “TAIR10.27” under /var/www/JBrowse/JBrowse-1.11.6/data. Then create two folders - “genome” and “gff” - under the reference genome folder (/var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27).
        * Download the TAIR10.27 genome (or any reference genome) from [Ensembl](ftp://ftp.ensemblgenomes.org/pub/plants/release-27/fasta/arabidopsis_thaliana/dna/). Download each chromosome separately, and then unzip them and put into the appropriate reference genome folder, e.g. /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome  (Note: only unzipped chromosome files should be put in the /www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome/ folder).
        * Concatenate the genome into a single FASTA file. Model your commands after the following example:
@@ -70,7 +70,7 @@
           ./bin/prepare-refseqs.pl --fasta data/TAIR10.27/genome/TAIR10.27.fa --out data/TAIR10.27/
           ./bin/flatfile-to-json.pl --gff data/TAIR10.27/gff/TAIR10.27.gff3 --type transcript --trackLabel transcript --out data/TAIR10.27**
        * Access http://localhost/JBrowse/JBrowse-1.11.6/?data=data/TAIR10.27 to check that you have sucessfully added TAIR10 genome to JBrowse 
-       * ########################################################################
+       * ######################################################################## 
        * Enter the following commands into the command line:
          ** cd /var/www/JBrowse/JBrowse-1.11.6/data/
           sudo chgrp www-data userData/

Home modified by Houxiang Zhu

Houxiang Zhu — Tue, 22 Dec 2015 16:31:00 -0000

--- v69
+++ v70
@@ -58,6 +58,7 @@
           ./setup.sh**
        * Create a folder called “data” under /var/www/JBrowse/JBrowse-1.11.6 
        * Create a folder called “userData” under /var/www/JBrowse/JBrowse-1.11.6/data.
+       * ###To add any new reference genome, repeat steps in this block. Change “TAIR10.27” in this block to the reference genome that you want to add###
        * To add a reference genome, also create a folder under /var/www/JBrowse/JBrowse-1.11.6/data. For example: create a folder called “TAIR10.27” under /var/www/JBrowse/JBrowse-1.11.6/data. Then create two folders - “genome” and “gff” - under the reference genome folder (/var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27).
        * Download the TAIR10.27 genome (or any reference genome) from [Ensembl](ftp://ftp.ensemblgenomes.org/pub/plants/release-27/fasta/arabidopsis_thaliana/dna/). Download each chromosome separately, and then unzip them and put into the appropriate reference genome folder, e.g. /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome  (Note: only unzipped chromosome files should be put in the /www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome/ folder).
        * Concatenate the genome into a single FASTA file. Model your commands after the following example:
@@ -69,6 +70,7 @@
           ./bin/prepare-refseqs.pl --fasta data/TAIR10.27/genome/TAIR10.27.fa --out data/TAIR10.27/
           ./bin/flatfile-to-json.pl --gff data/TAIR10.27/gff/TAIR10.27.gff3 --type transcript --trackLabel transcript --out data/TAIR10.27**
        * Access http://localhost/JBrowse/JBrowse-1.11.6/?data=data/TAIR10.27 to check that you have sucessfully added TAIR10 genome to JBrowse 
+       * ########################################################################
        * Enter the following commands into the command line:
          ** cd /var/www/JBrowse/JBrowse-1.11.6/data/
           sudo chgrp www-data userData/

Home modified by Houxiang Zhu

Houxiang Zhu — Tue, 22 Dec 2015 16:24:47 -0000

--- v68
+++ v69
@@ -59,11 +59,11 @@
        * Create a folder called “data” under /var/www/JBrowse/JBrowse-1.11.6 
        * Create a folder called “userData” under /var/www/JBrowse/JBrowse-1.11.6/data.
        * To add a reference genome, also create a folder under /var/www/JBrowse/JBrowse-1.11.6/data. For example: create a folder called “TAIR10.27” under /var/www/JBrowse/JBrowse-1.11.6/data. Then create two folders - “genome” and “gff” - under the reference genome folder (/var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27).
-       * Download the TAIR10 genome (or any reference genome) from [Ensembl](ftp://ftp.ensemblgenomes.org/pub/plants/release-27/fasta/arabidopsis_thaliana/dna/). Download each chromosome separately, and then unzip them and put into the appropriate reference genome folder, e.g. /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome  (Note: only unzipped chromosome files should be put in the /www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome/ folder).
+       * Download the TAIR10.27 genome (or any reference genome) from [Ensembl](ftp://ftp.ensemblgenomes.org/pub/plants/release-27/fasta/arabidopsis_thaliana/dna/). Download each chromosome separately, and then unzip them and put into the appropriate reference genome folder, e.g. /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome  (Note: only unzipped chromosome files should be put in the /www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome/ folder).
        * Concatenate the genome into a single FASTA file. Model your commands after the following example:
           **cd /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome
           cat * > TAIR10.27.fa**
-       * Download the TAIR10 (or other reference genome) gff file from [Ensembl](ftp://ftp.ensemblgenomes.org/pub/plants/release-27/gff3/arabidopsis_thaliana/). In this case you may directly download the entire gff file (rather than by individual chromosome), e.g. “Arabidopsis_thaliana.TAIR10.27.gff3.gz”. Unzip and rename it to “TAIR10.27.gff3” and put the file into /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/gff 
+       * Download the TAIR10.27 (or other reference genome) gff file from [Ensembl](ftp://ftp.ensemblgenomes.org/pub/plants/release-27/gff3/arabidopsis_thaliana/). In this case you may directly download the entire gff file (rather than by individual chromosome), e.g. “Arabidopsis_thaliana.TAIR10.27.gff3.gz”. Unzip and rename it to “TAIR10.27.gff3” and put the file into /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/gff 
        * Configure JBrowse with your reference genome. Model your commands after the following example:
           **cd /var/www/JBrowse/JBrowse-1.11.6
           ./bin/prepare-refseqs.pl --fasta data/TAIR10.27/genome/TAIR10.27.fa --out data/TAIR10.27/

Home modified by Houxiang Zhu

Houxiang Zhu — Mon, 14 Dec 2015 09:22:30 -0000

--- v67
+++ v68
@@ -80,7 +80,7 @@
 * Download [ct-finder.zip](https://sourceforge.net/projects/ct-finder/files/latest/download) and unzip it. Put it into the root directory of the apache server (e.g. /var/www/ on Debian or Ubuntu systems, /var/www/html on Red Hat, Fedora, or SUSE. /var/www/ is used as an example in this guide).
 * Create a folder named according to the genome name that you want to add under /var/www/ct-finder/bowtie2db/. E.g. “TAIR10.27” under /var/www/ct-finder/bowtie2db/.
 * Copy the TAIR10 genome (TAIR10.27.fa) from /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome/ folder into /var/www/ct-finder/bowtie2db/TAIR10.27/ folder.
-* Create a .txt file called “TAIR10.27_chr.txt”, including TAIR10 chromosome names, in the /var/www/ct-finder/bowtie2db/TAIR10.27/ folder. Refer to the format in /var/www/ct-finder/example/TAIR10.27_chr.txt.
+* Create a .txt file called “TAIR10.27_chr.txt”, including TAIR10 chromosome names, in the /var/www/ct-finder/bowtie2db/TAIR10.27/ folder (Note: all chromosome names in “TAIR10.27_chr.txt” file must be the same as the names in "TAIR10.27.fa" file). Refer to the format in /var/www/ct-finder/example/TAIR10.27_chr.txt.
 * Build the bowtie2 index. This may take some time, depending on the size of the reference genome. Model your commands after the following examples:
    **cd /var/www/ct-finder/bowtie2db/TAIR10.27/
    bowtie2-build TAIR10.27.fa TAIR10.27**

Home modified by Houxiang Zhu

Houxiang Zhu — Mon, 14 Dec 2015 09:03:35 -0000

Home modified by Houxiang Zhu

Houxiang Zhu — Mon, 14 Dec 2015 09:02:16 -0000

--- v65
+++ v66
@@ -94,4 +94,5 @@
        * JBROWSE_RELATIVE_PATH: set the relative path for folder “JBrowse-1.11.6” in JBrowse. Here it is relative to /var/www/ (the default apache root directory). 
        * JBROWSE_DATA_PATH: set the absolute path for folder “Data” in JBrowse. 
        * JBROWSE_USERDATA_RELATIVE_PATH: set the relative path for folder “userData” in JBrowse. Here it is relative to /var/www/ct-finder/proc/. 
+* Enter http://localhost/ct-finder/ into the browser to run CT-Finder.

Home modified by Houxiang Zhu

Houxiang Zhu — Mon, 14 Dec 2015 07:58:36 -0000

--- v64
+++ v65
@@ -30,6 +30,8 @@
 * [Perl](http://www.perl.org/) (version: 5.18.2)
    You most likely already have perl installed. Type **perl -v** into the command line to find out which version. 

 
 * [PHP](https://www.php.net/)
+   Enter the following commands into the command line:
+       * **sudo apt-get update**
        * **sudo apt-get install libapache2-mod-php5**
        * **sudo a2enmod php5** 
        * **sudo service apache2 restart**
@@ -77,11 +79,15 @@
 * TAIR10 will be used as the example reference genome in this manual. Change names of folders and files as appropriate for the reference genome you are using.
 * Download [ct-finder.zip](https://sourceforge.net/projects/ct-finder/files/latest/download) and unzip it. Put it into the root directory of the apache server (e.g. /var/www/ on Debian or Ubuntu systems, /var/www/html on Red Hat, Fedora, or SUSE. /var/www/ is used as an example in this guide).
 * Create a folder named according to the genome name that you want to add under /var/www/ct-finder/bowtie2db/. E.g. “TAIR10.27” under /var/www/ct-finder/bowtie2db/.
-* Copy the TAIR10 genome (TAIR10.27.fa) from /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome/ folder into /var/www/ct-finder/bowtie2db/ TAIR10.27/ folder.
+* Copy the TAIR10 genome (TAIR10.27.fa) from /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome/ folder into /var/www/ct-finder/bowtie2db/TAIR10.27/ folder.
 * Create a .txt file called “TAIR10.27_chr.txt”, including TAIR10 chromosome names, in the /var/www/ct-finder/bowtie2db/TAIR10.27/ folder. Refer to the format in /var/www/ct-finder/example/TAIR10.27_chr.txt.
 * Build the bowtie2 index. This may take some time, depending on the size of the reference genome. Model your commands after the following examples:
    **cd /var/www/ct-finder/bowtie2db/TAIR10.27/
    bowtie2-build TAIR10.27.fa TAIR10.27**
+* Change TAIR10.27 folder ownership and permissions using the following commands:
+   **cd /var/www/ct-finder/bowtie2db/
+   sudo chgrp www-data TAIR10.27
+   sudo chmod g+rwx TAIR10.27**
 * Go to /var/www/ct-finder/interface folder to edit the files “Cas9.php”, “Cas9n.php” and “RFNs.php”. Open “Cas9.php”, and then add one line of code “<option value=TAIR10.27 >Ensembl Thale cress (Arabidopsis thaliana) genome TAIR10.27</option>” below “<option value=none>Choose an organism</option>” (Note: the "TAIR10.27" in "value=TAIR10.27" is the name of your reference genome folder). Do the same for “Cas9n.php” and “RFNs.php”.
 * Go to /var/www/ct-finder/ folder to edit “root_path.php” file. Open it and Configure the following parameters to reflect the actual location paths in your setup:
        * JBROWSE_USERDATA_PATH: set the absolute path for folder “userData” in JBrowse.

Home modified by Houxiang Zhu

Houxiang Zhu — Sat, 12 Dec 2015 04:03:15 -0000

--- v63
+++ v64
@@ -77,7 +77,7 @@
 * TAIR10 will be used as the example reference genome in this manual. Change names of folders and files as appropriate for the reference genome you are using.
 * Download [ct-finder.zip](https://sourceforge.net/projects/ct-finder/files/latest/download) and unzip it. Put it into the root directory of the apache server (e.g. /var/www/ on Debian or Ubuntu systems, /var/www/html on Red Hat, Fedora, or SUSE. /var/www/ is used as an example in this guide).
 * Create a folder named according to the genome name that you want to add under /var/www/ct-finder/bowtie2db/. E.g. “TAIR10.27” under /var/www/ct-finder/bowtie2db/.
-* Copy the TAIR10 genome “TAIR10.27.fa” from /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome/ folder into /var/www/ct-finder/bowtie2db/ TAIR10.27/ folder.
+* Copy the TAIR10 genome (TAIR10.27.fa) from /var/www/JBrowse/JBrowse-1.11.6/data/TAIR10.27/genome/ folder into /var/www/ct-finder/bowtie2db/ TAIR10.27/ folder.
 * Create a .txt file called “TAIR10.27_chr.txt”, including TAIR10 chromosome names, in the /var/www/ct-finder/bowtie2db/TAIR10.27/ folder. Refer to the format in /var/www/ct-finder/example/TAIR10.27_chr.txt.
 * Build the bowtie2 index. This may take some time, depending on the size of the reference genome. Model your commands after the following examples:
    **cd /var/www/ct-finder/bowtie2db/TAIR10.27/