- galaxy-user - lists.galaxyproject.org

Galaxy STARTUP ERROR!
by giovanni pascarella 02 Oct '13

02 Oct '13

Hi! I am trying to launch Galaxy locally but I'm getting the following error: tkx417:galaxy pascarellagiovanni$ sh run.sh Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py", line 220, in run result = self.command() File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py", line 643, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 374, in loadobj global_conf=global_conf) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext global_conf=global_conf) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 561, in get_context section) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 620, in _context_from_explicit value = import_string(found_expr) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string return pkg_resources.EntryPoint.parse("x=" + s).load(False) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/web/__init__.py", line 4, in <module> from framework import expose File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/web/framework/__init__.py", line 40, in <module> from babel.support import Translations File "/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/support.py", line 29, in <module> from babel.dates import format_date, format_datetime, format_time, LC_TIME File "/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/dates.py", line 34, in <module> LC_TIME = default_locale('LC_TIME') File "/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/core.py", line 642, in default_locale return '_'.join(filter(None, parse_locale(locale))) File "/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/core.py", line 763, in parse_locale raise ValueError('expected only letters, got %r' % lang) ValueError: expected only letters, got 'utf-8' Anybody knows what this is about? Thanks, Giovanni

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Re: [galaxy-user] main galaxy server is down?
by Jennifer Jackson 01 Oct '13

01 Oct '13

Hi Boaz, The NGS queue was believed to be moving yesterday (incorrectly by me), and is now under review again. The grey queued jobs will eventually execute, so I wouldn't delete them quite yet, but jobs are not processing at this time. We will update the banner on the public Main server if this is extended. http://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute For high-priority work, a move to an alternate Galaxy solution is an option. A cloud Galaxy is one good choice - this is a sure thing but has associated costs. Other public servers are also potential choices - each has different tools available and other requirements - so check out these and see what may work. Links for you to review are here: http://wiki.galaxyproject.org/BigPicture/Choices http://wiki.galaxyproject.org/Cloud http://wiki.galaxyproject.org/PublicGalaxyServers Good luck, and thanks for the patience during our upgrade, Jen Galaxy team On 10/1/13 1:53 AM, Boaz Shaanan wrote: > Thanks Jennifer, My job is still in the queue, so I'll keep it that way. From other people's complaints, it looks as if it's the mapping jobs that mostly have problems (mine is one like that too - a Lastz run). Any particular reason or just the general server performance issue. > > Thanks, > > Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > ________________________________________ > From: Jennifer Jackson [jen(a)bx.psu.edu] > Sent: Tuesday, October 01, 2013 12:27 AM > To: בעז שאנן > Cc: galaxy-user(a)lists.bx.psu.edu > Subject: Re: [galaxy-user] main galaxy server is down? > > Hello Boaz, > > Performance should be improved by now. Please allow your jobs to run if > still queued. If any error due to fileserver or cluster issues, please > simply re-run. Our apologies for these inconveniences, improvements are > due very soon! > > Best, > > Jen > Galaxy team > > On 9/27/13 2:37 PM, Boaz Shaanan wrote: >> Hi, >> >> Is the main galaxy server down? Or very sloooow? I have a Lastz job (not too demanding and one that has been run several times before) waiting for a long time already. >> >> Thanks, >> >> Boaz >> >> >> >> Boaz Shaanan, Ph.D. >> Dept. of Life Sciences >> Ben-Gurion University of the Negev >> Beer-Sheva 84105 >> Israel >> >> E-mail: bshaanan(a)bgu.ac.il >> Phone: 972-8-647-2220 Skype: boaz.shaanan >> Fax: 972-8-647-2992 or 972-8-646-1710 >> >> >> >> >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ > -- > Jennifer Hillman-Jackson > http://galaxyproject.org > > -- Jennifer Hillman-Jackson http://galaxyproject.org

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problem with logging in after resetting password
by Siew-Lan Ang 01 Oct '13

01 Oct '13

Hello, I am having problems accessing my galaxy account. I forgot my password and asked for it to be reset. When the new password was sent to me, it didn't work when I tried it. I've resetted 4x and each time the new password hasn't worked to log. Hope you can solve the problem. Regards, Siew-Lan Ang ____________________ Siew-Lan Ang NIMR The Ridgeway London, NW7 1AA UK Tel: 44 (0)2088162426 Fax: 44 (0)2088162523

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bwa indexing not automatic?
by Joshua Orvis 30 Sep '13

30 Sep '13

I installed a new copy of galaxy today and then added the bwa_wrappers tool. After I upload my reference genome and left/right reads I get output like this each time I try to run bwa for illumina: The alignment failed. Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwt_restore_bwt] fail to open file '/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat.bwt'. Abort! /bin/sh: line 1: 11607 Aborted bwa aln -t 4 -I /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_2.dat > /tmp/tmpMuj4l2/tmpUIdxXT If I manually do the 'bwa index' command on dataset_4.dat it works but in the past this seemed to happen automatically. Any clue what's going on here?

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main galaxy server is down?
by garzetti 30 Sep '13

30 Sep '13

I have the same problem with the BWA mapping tool (jobs waiting for run since Friday), but other tools (e.g. SAMtools) are working. My analysis also depends a lot on these mapping data! Debora > Message: 1 > Date: Sat, 28 Sep 2013 16:47:01 +0000 > From: "Yardley, Nathan" <ny2217(a)cumc.columbia.edu> > To: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> > Subject: Re: [galaxy-user] main galaxy server is down? > Message-ID: > <9633FF819ABAF94A82A38D94B64B664501291F43(a)SGWAEXM003.mc.cumc.columbia.edu> > > Content-Type: text/plain; charset="us-ascii" > > I'm wondering the same. I have a mapping job that hasn't moved into the queue since I put it there on Thursday. It's the last sample set I need to move forward with some analysis and I've been trying to get it for more than a week now. :/ > > Nathan > ________________________________________ > From: galaxy-user-bounces(a)lists.bx.psu.edu [galaxy-user-bounces(a)lists.bx.psu.edu] on behalf of Boaz Shaanan [bshaanan(a)bgu.ac.il] > Sent: Friday, September 27, 2013 5:37 PM > To: galaxy-user(a)lists.bx.psu.edu > Subject: [galaxy-user] main galaxy server is down? > > Hi, > > Is the main galaxy server down? Or very sloooow? I have a Lastz job (not too demanding and one that has been run several times before) waiting for a long time already. > > Thanks, > > Boaz > > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaanan(a)bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > -- Debora Garzetti, PhD Student AG Rakin Max von Pettenkofer-Institute, LMU Pettenkoferstraße 9A 80336 Munich E-mail: garzetti(a)mvp.uni-muenchen.de Phone: +49 (0)89 2180 72915

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main galaxy server is down?
by Boaz Shaanan 30 Sep '13

30 Sep '13

Hi, Is the main galaxy server down? Or very sloooow? I have a Lastz job (not too demanding and one that has been run several times before) waiting for a long time already. Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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October Galaxy Update Newsletter is out
by Dave Clements 30 Sep '13

30 Sep '13

Hello all, The October 2013 Galaxy Update is out<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10> : *Highlights:* - A record *six new public servers<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#New_Public_Servers> * - 44 new papers<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#New_Papers> - Open Positions<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Who.27s_Hiring> at nine different organizations - Upcoming Events<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Events>, lots of them in Australia<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Australia.21> plus 3 other continents<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#All_Those_Other_Contine…>. - Online materials from past events<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Online_Materials_from_P…>, including all GCC2013 videos on Vimeo <http://bit.ly/gcc2013vimeo> and course materials for the 2013 UC Davis Bioinformatics Short Course<http://bit.ly/16rAUkf>. The UC Davis course featured 5 great days of lecture and hands-on exercises. - More Tool Shed contributions<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Tool_Shed_Contributions> than you can shake a stick at. If you have anything you would like to see in the next *Galaxy Update<http://wiki.galaxyproject.org/GalaxyUpdates> *, please let us know. Dave Clements and the Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Built-in Editor
by Isaac Knoflicek 30 Sep '13

30 Sep '13

Is it possible to use ACE or some other type of in line editor to modify files in Galaxy? Like if we had a tool that accepted as a parameter a file written in a homegrown modeling language, is there any way to update that file without downloading and re-uploading? Has anyone seen or done anything like this? Thanks, Isaac Knoflicek IT Manager - Laboratory of Genetics University of Wisconsin - Madison

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How to become admin on Galaxy Cloudman
by Yan He 30 Sep '13

30 Sep '13

Hi all, I just established Galaxy Cloudman on Amazon EC2. I would like to add some tools in tool shed to to it. However, I need to be the admin to do this. Once I got into the galaxy cloudman, I had to register a new account and then log in. The admin interface (described in tool shed wiki) didn't appear at all. How could I log in as admin on Galaxy Cloudman? This may be a very simple question, but it bothers me two days. Looking forward to your replies! Best wishes, Yan

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SNP calling problems
by garzetti 27 Sep '13

27 Sep '13

Dear all, I have been looking for an answer to my problem in all the Galaxy Support resources but with no success. I am sorry if this topic has been already discussed! So, I am analyzing MiSeq data on the main Galaxy. I have Fastq files from 4 paired-end samples. After having checked the quality with FastQC and groomed them, I have performed a BWA mapping, filtered the results and converted the SAM to BAM files (for each sample separately). I have then called SNPs with Freebayes and SAMtools, encountering problems in both cases. 1) SAMtools: if I run the Generate pileup tool, then the Filter pileup doesn't recognize any valid format in the files I have in my History and I cannot go on with the analysis. Why is that? What can I do? 2) I have performed variant calling with Freebayes on single BAM files and on one merged BAM files from all my four BWA mapping files. In all cases, the last column is "unknown", while it should be the name of my sample. This is not a big deal for the single vcf files, but from the merged BAM file, I cannot discriminate from which sample the SNPs were detected. I think there is a problem in the BAM files which are not properly indexed. Also Freebayes needs an RG tag. Is there a tool in Galaxy I can use to index BAM files, adding the RG tag? I hope someone can help me! Thank you very much! Debora -- Debora Garzetti, PhD Student AG Rakin Max von Pettenkofer-Institute, LMU Pettenkoferstraße 9A 80336 Munich E-mail: garzetti(a)mvp.uni-muenchen.de Phone: +49 (0)89 2180 72915

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