Staden Package Activity
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Activity for Staden Package
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Christopher Daechert posted a comment on discussion Open Discussion
Hey, I found this old thread using the search function. I encountered the very same problem and actually in our case the problem was a umlaut/mutated vowel ("ä") in the file path. omg. Took me hours to find out. So maybe in your case, @JongKyu Lee, it is the "-". Cheers and thanks Chris
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Alex Byrne modified a comment on discussion Open Discussion
Hello, I have many (total approx 30,000) old .scf files that I need to use with modern software that only accepts scf 2.9 and greater. Trev is able to convert the files to SCF 3 for me, but as far as I can work out only one at a time - what would you recommend for batch conversion? Edit: mistake in the title, should read SCF 2 to SCF 3 !
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Hello, I have many (total approx 30,000) old .scf files that I need to use with modern software that only accepts scf 2.9 and greater. Trev is able to convert the files to SCF 3 for me, but as far as I can work out only one at a time - what would you recommend for batch conversion?
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Hello, I have many (total approx 30,000) old .scf files that I need to use with modern software that only accepts scf 2.9 and greater. Trev is able to do this for me, but as far as I can work out only one at a time - what would you recommend for batch conversion?
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Enrico Perez posted a comment on discussion Open Discussion
I just found out that I need to reinstall XQuartz and make sure I run the files from the bin folder in the staden package. It works in Big Sur. Hurray! Thank you Best wishes, J On 9 Dec 2020, at 17:17, Enrico Perez enricoperez2001@users.sourceforge.net wrote: Thank you for replying so soon. Yes. I tried that on Mojave. I didn’t think of doing that on Big Sur. Bit I will try now. Thank you for your reply. I am with you about paying to develop. I think it is wrong and just to say that I love your...
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Thank you for replying so soon. Yes. I tried that on Mojave. I didn’t think of doing that on Big Sur. Bit I will try now. Thank you for your reply. I am with you about paying to develop. I think it is wrong and just to say that I love your stamen package. I have not seen anything else better since 2003. Thank you Thank you Best wishes, J On 9 Dec 2020, at 15:40, James Bonfield jkbonfield@users.sourceforge.net wrote: Unfortunately I no longer have access to a Mac so this is simply impossible for...
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James Bonfield posted a comment on discussion Open Discussion
Unfortunately I no longer have access to a Mac so this is simply impossible for me to do. The software hasn't changed in years, so this is an Apple OS change which has broken the software. From what I've been told by others the problem is that the application isn't signed so Apple now consider it unsafe. In order to fix this we'd need to pay apple to become an official developer that is able to sign their applications, I think... but I don't do apple development so I don't really know. However one...
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Staden package is the most awsome multiple sequence alignment. Free - checked Using your abi files - checked but for the past few updated versions of the Mac OS Catalina, and Big Sur this package is not functional. I am not computer wise so I do not know if I am doing something wrong. I tried to install from source but again I am not computer wise. I will probably need someone to tell me do this code and then that code and voila! I have upgraded all my other computers to Big Sur from Mojave (I wanted...
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Added -j/-J options to tg_index.
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Fixed a data type overflow in Find Oligos when the total length of
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Fixed long-standing SAM pileup bug.
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Fix crash in gap5_cmd script.
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Fix a crash when disassembling entire contigs.
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Added a tg_index "-Q qual" option to override quality.
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Fixed 32-bit rec bug for cache_exists()
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List Base Confidence improvements.
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Updated restriction enzyme files.
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Daniel modified a comment on discussion Open Discussion
Dear Friends, I am trying to produce a consensus from a set of contigs I have assembled. I generated exp files from pregap4 by just "Add Files" and then "Run". When I try to open this "pregap.passed" files in gap4, it says this in the output window of gap4: Automatic sequence assembler Processing 1 in batch File name 88161_cov_51.043267.exp Reading length 88055 New reading does not overlap: start a new contig This gel reading has been given the number 1 Processing 2 in batch File name 88156_cov_48.969578.exp...
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Dear Friends, I am trying to produce a consensus from a set of contigs I have assembled. I generated exp files from pregap4 by just "Add Files" and then "Run". When I try to open this "pregap.passed" files in gap4, it says this in the output window of gap4: Automatic sequence assembler Processing 1 in batch File name 88161_cov_51.043267.exp Reading length 88055 New reading does not overlap: start a new contig This gel reading has been given the number 1 Processing 2 in batch File name 88156_cov_48.969578.exp...
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Dear Friends, I am trying to produce a consensus from a set of contigs I have assembled. I generated exp files from pregap4 by just "Add Files" and then "Run". When I try to open this "pregap.passed" files on gap4, it says this in the output window of gap4: Automatic sequence assembler Processing 1 in batch File name 88161_cov_51.043267.exp Reading length 88055 New reading does not overlap: start a new contig This gel reading has been given the number 1 Processing 2 in batch File name 88156_cov_48.969578.exp...
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Dear Friends, I am trying to produce a consensus from a set of contigs I have assembled. I generated exp files from pregap4 by just "Add Files" and then "Run". When I try to open this "pregap.passed" files on gap4, it says this in the output window of gap4: **~~~ Gap4 has started up in 'Beginner' mode. To select another menu level, please use the 'Configure menus' command in the 'Options' menu. ============================================================ Tue 26 Feb 19:21:29 2019: open database ------------------------------------------------------------...
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Dear Friends, I am trying to produce a consensus from a set of contigs I have assembled. I generated exp files from pregap4 by just "Add Files" and then "Run". When I try to open this "pregap.passed" files on gap4, it says this in the output window of gap4: Gap4 has started up in 'Beginner' mode. To select another menu level, please use the 'Configure menus' command in the 'Options' menu. ============================================================ Tue 26 Feb 19:21:29 2019: open database ============================================================...
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Dear Friends, I am trying to produce a consensus from a set of contigs I have assembled. I generated exp files from pregap4 by just "Add Files" and then "Run". When I try to open this "pregap.passed" files on gap4, it says this in the output window of gap4: Gap4 has started up in 'Beginner' mode. To select another menu level, please use the 'Configure menus' command in the 'Options' menu. ============================================================ Tue 26 Feb 19:21:29 2019: open database ============================================================...
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Dear Friends, I am trying to produce a consensus from a set of contigs I have assembled. I generated exp files from pregap4 by just "Add Files" and then "Run". When I try to open this "pregap.passed" files on gap4, it says this in the output window of gap4: Gap4 has started up in 'Beginner' mode. To select another menu level, please use the 'Configure menus' command in the 'Options' menu. ============================================================ Tue 26 Feb 19:21:29 2019: open database ============================================================...
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Alexandra Jane Schuessler posted a comment on discussion Open Discussion
Hello, I am trying to run PreGap4 on my windows 10, I keep getting an error when I run my sequences that is "child killed". It is only happening to my forward sequence and is happening consistently. The files are in the correct format and the sequences are clean. I am wondering if this is a bug with the program and if I can possibly fix it. Thanks.
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Make Read #Numbers to Names work for contigs too.
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Our Mac laptop happens to have /usr/local/lib/libtk8.6.dylib already there, presumably due to one of the Apple package managers such as Homebrew. Sadly we have no admin rights so can't experiment, but we're trying to rectify this. Maybe using Homebrew yourself and installing Tk will solve this, but in theory our drive image should be self contained so there is something wrong in our package too.
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Hari Om Pandey posted a comment on discussion Open Discussion
Hello help me out! Not good at working with unix environment. Followed Last edit: John Nash 2015-01-06 to build Staden package on MacOS Mozave tried to run $gap5; got following message dlopen(/usr/local/lib/libtk8.6.dylib, 6): Library not loaded: /opt/local/lib/libXft.2.dylib Referenced from: /usr/local/lib/libtk8.6.dylib Reason: image not found
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It's been many years since I created the MacOSX .dmg image, so I can't be sure it even works on modern versions of MacOS. In theory it was meant to launch the program, but it may not work without a version of X11 running already. I don't have time any more for updating the package other than small components like "io_lib", so this isn't something I can fix myself. However can you try running the programs by full path from a Terminal window? It may be it still works fine in that situation. Remember...
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Juan Esteban Zurita modified a comment on discussion Open Discussion
Hi, I need to edit some sequences but am completely new to the open source programming environment. I am using High Sierra version 10.13.6. I think I don't understand how to install the package correctly. I have followed some old instructions (like this one: https://sourceforge.net/p/staden/discussion/347718/thread/d36794a2/) but I still cannot make it. I attached a screenshot of how the icons of gap4, pregap4, gap5, etc appear in the Applications folder. It is like the computer does not recognize...
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Hi, I need to edit some sequences but am completely new to the open source programming environment. I am using High Sierra version 10.13.6. I think I don't understand how to install the package correctly. I have followed some old instructions (like this one: https://sourceforge.net/p/staden/discussion/347718/thread/d36794a2/) but I still cannot make it. I attached a screenshot of how the icons of gap4, pregap4, gap5, etc appear in the Applications folder. It is like the computer does not recognize...
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Hi, I need to edit some sequences but am completely new to the open source programming environment. I am using High Sierra version 10.13.6. I think I don't understand how to install the package correctly. I have followed some old instructions (like this one: https://sourceforge.net/p/staden/discussion/347718/thread/d36794a2/) but I still cannot make it. I attached a screenshot of how the icons of gap4, pregap4, gap5, etc. It is like the computer does not recognize them as software or something like...
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caowm2001 posted a comment on ticket #110
Sorry wrong patch, should be: --- src/mutlib/trace.cpp 2005-04-27 16:17:35 +0000 +++ - @@ -953,20 +953,21 @@ // Compute the mode by counting the maximum run length int nRun = 0; int nRunMax = 0; int nLast = -1; m_nIntervalMode = 0; for( n=0; n<nBases; n++ ) { if( Interval[n] == nLast ) nRun++; else { if( nRun > nRunMax ) { m_nIntervalMode = nLast; nRunMax = nRun; } nRun = 1; nLast = Interval[n]; } } + if( nRun > nRunMax ) m_nIntervalMode = nLast;
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mutlib/trace.cpp: wrong interval mode compute
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If you're not looking to do interactive editing and finishing, then Gap4 (and indeed Gap5) aren't the ideal tool and I would thoroughly recommend BAM/CRAM instead as it's what most tools cope with now. The burden of using gap4/5 isn't worth it without the requirement of being able to do on-the-fly editing. SAM et al are really designed around references, but contigs are sufficient still to act in the same purpose provided you don't go over several million ish mark, at which point the 2Gb size limit...
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Will Stokes posted a comment on discussion Open Discussion
Thanks, I appreciate the frank assessment of the original staden codebase. In addition to Phrap I'm also looking into AMOS which looks promising. I was originally contemplating using Lucy to clean my data before passing it to an assembler and am not yet sure how to best (or if I even need to) do that with AMOS. I have had some success with AMOS and am also looking into using samtools or htslib to convert from SAM to BAM or CRAM. I'm presently not dealing with NGS data but would like to future proof...
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Sadly the Staden Package is largely unsupported now, barring bug fixes perhaps if something major and simple cropped up. It's simply a matter of time, most of which is now spent maintaining samtools et al and the CRAM code. Regarding Gap4 (and gap5 for that matter), it is inherently tied to tcl/tk. The main GUI of Gap4 is Tcl/Tk with the actual functionality written in C and then providing new Tcl commands to execute those C functions. This provides an easy scripting environment while also maintaining...
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Hi, I'm looking into the feasibility of using the gap4 algorithm from C code. I understand the exp format and can already generate such files myself. I'm not looking into gap4 and and finding documentation like this: http://staden.sourceforge.net/scripting_manual/scripting_111.html to be a bit out of date. E.g. there is no io.c (it now appears to be io1.c) and I cannot find a mk directory or a gap4_defs.mk file. I have been exploring setting up a project to build a subset of the gap4 (and related...
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Added more primer3 configurables to the GUI.
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Bruna posted a comment on discussion Open Discussion
Hi there, I'm a new user of Staden, I have a little problem and I couldn't find the answer yet. I have two clones, sequenced with both For and Rev primers. Why Gap4 didn't put them as a unique contig? In contig selector I have two contigs, not one as expected. I know for sure they are the same, one is in the right orientation and the other in opposite orientation. Do you know how I could set a contig as the opposite orientation of the other, is Gap4 capable of doing it automatically or it is not...
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Remove a spurious -reading option when invoking the contig editor from
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Staden Package released /io_lib/1.14.9/io_lib-1.14.9.tar.gz
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Io_lib (aka libstaden-read.so on Debian systems) migrated to github
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Fixed a rare renormalisation bug in the rANS co...
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Disable the unsorted position mode for multi-re...
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Fix BAM bin value for placed but unmapped reads...
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Added code to detect if two consecutive quality...
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Added a dedup mode (with rANS1 encoding) for qu...
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Bug fix to codec timing reports.
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Updated for libbsc 3.1.0.
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Added debug code for aggregating the time spent...
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Fixed a CRAM encoder crash when no @SQ lines ar...
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Removed a CRAM encoding crash.
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Fixed a compression inefficiency when switching...
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Bug fixes with small data.
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Migrated codec specific files into their own di...
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Prints external codec types
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Switch to EXTERNAL for unsorted AP data series.
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Removed an uninitialised memory access, althoug...
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Merged in the cram_filter branch.
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Merged trunk r4100 into branch.
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Improved multi-threaded CRAM decoding.
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Moved the block CRC32 checking from within bloc...
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Add io_lib/bgzip.h to pkginclude_HEADERS
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Added a Scramble -q option to omit updating the...
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The SAM/CRAM header blocks are now kepted in th...
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Added more debugging.
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Added a '%X' format string to show the library ...
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Added experimental support for bgzip-ed fasta r...
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Also enabled -! (BAM_OPT_IGNORE_CHKSUM) for the...
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Added CRC checking for BAM files.
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Fixed a crash in ref MD5 creation when sequence...
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OS X fails 5/10 tests
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Fixed in commit 4089: https://sourceforge.net/p/staden/code/4089/ It's trivial to...
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Added dependencies to the scramble tests so tha...
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Fixed missing strchr prototype
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I can verify this locally. The test framework is auto-generated by Automake, so I...
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Hanspeter Niederstrasser posted a comment on ticket #109
New detail: if I run make -j1 check, then all the tests pass. So it seems to that...
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OS X fails 5/10 tests
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Fixed file descriptor leak in refs_load_fai().
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Fixed ancient and broken POPEN code. I don't k...
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Thanks, I appreciate the quick reply and suggestion. Will Stokes Chief Software Architect...
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On Mon, May 23, 2016 at 01:12:39PM +0000, Will Stokes wrote: Does Staden io_lib support...
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Does Staden io_lib support reading FASTQ content into a Read object? If not, can...
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Added use of mallopt M_TOP_PAD parameter and ap...
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Major decoding speed update.
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Made CRAM compression level 1 faster, at the ex...
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Added key ` (grave) binding in the contig edito...
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Bulk Rename Contig now accepts lists of reading...
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Added -unique_ends option to gap5_cmd FIJ.
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Cram file input 'Unkown sort order'
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Release 2.0.0b11
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Staden Package 2.0.0b11-2016 released
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Staden Package 2.0.0b11-2016 released
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