April 2012 - galaxy-dev - lists.galaxyproject.org

Galaxy version / Mercurial
by Sarah Maman 09 May '12

09 May '12

Hello, I would like to get source code with Mercurial of this tarballs : galaxy-dist.b258de1e6cea.tar.gz, and not the latest source. Is it possible to specify "b258de1e6cea" version with hg clone command ? The aim is to update my copy of Galaxy wich have been locally installed with a tarball in order to use, in the future, Mercurial and hg pull to update Galaxy version. Thanks a lot, Sarah Maman

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Migrating Workflows and Other Data to New Galaxy Instance
by Robert Chase 04 May '12

04 May '12

Hello, We are going to migrate to a new instance of the galaxy server. Our current instance contains a number of workflows and other data that we would like to have available on the new server. Is there a way to backup the workflows and then reload them on the new server? Regards, -Robert Paul Chase Channing Lab

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How to customize Galaxy web interface?
by Pascal Maugeri 03 May '12

03 May '12

Hi, I m running my own Galaxy instance and I would like to do some simple customization of the web interface such as adding my logos in the header frame, changing background colors, etc. I am having a look to static/ folders but I can't see clearly where the header frame is defined. Could you please tell me if there is any tutorial for doing so? Any starting point? Or which folder/file(s) corresponds to the web interface in the distribution? Best Regards, Pascal

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Unable to set BAM Metadata
by Ciara Ledero 01 May '12

01 May '12

This is my code for running a samtools command internally, via Galaxy: open INP,"< $ARGV[0]" or die "Cannot open file: $!"; $file = "$ARGV[1]"; open OUT, "> $file" or die "Cannot open file: $!"; @out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0] 2>&1`; print OUT @out; close INP; close OUT; The 2>&1 is used to redirect the STDERR to STDOUT. When I run this in the console, it gives a non-empty file. But when run it in Galaxy, Galaxy can no longer find the path. This error message is given to me. Traceback (most recent call last): File "/home/applications/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 126, in run_job job_wrapper.finish( stdout, stderr ) File "/home/applications/galaxy-dist/lib/galaxy/jobs/__init__.py", line 618, in finish dataset.set_meta( overwrite = False ) File "/home/applications/galaxy-dist/lib/galaxy/model/__init__.py", line 874, in set_meta return self.datatype.set_meta( self, **kwd ) File "/home/applications/galaxy-dist/lib/galaxy/datatypes/binary.py", line 179, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found The weird thing is, when I remove the 2>&1 from the code and run it again in Galaxy, I am able to get this diagnostic message: [samopen] SAM header is present: 66338 sequences. This is the reason why I added the 2>&1 in the first place, so that this diagnostic message would be 'ignored' (since it is detected as an error). Now, if the other code (the one without 2>&1) is able to produce the aforementioned diagnostic message, then I assume that it is able to at least execute the samtools command internally. But when I add the 2>&1, galaxy can no longer find the command. Do I need to specify a path somewhere in the galaxy-dist? I apologize for the very long message. Thanks in advance, CL

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how to get "macs" not "macs14" for Galaxy
by Sergei Manakov 01 May '12

01 May '12

Hello, I am trying to set up MACS tool on local Galaxy. Galaxy comes with it's macs-wrapper.py and macs-wrapper.xml, but it wants to use "macs" not "macs14" executable. I tried to to editing macs-wrapper.py to make it use "macs14" instead, but some options are not the same between the two, and the tool crashes. I would appreciate if someone could give me an advice on where I can get "macs" executable for 64-bit Linux. thanks, Sergei -- Sergei (Siarhei Manakou) Manakov California Institute of Technology +1 626 395 3593

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Remove libraries using Galaxy code or API
by liram_vardi＠agilent.com 01 May '12

01 May '12

Hello, I am using Galaxy API for some actions and I must say that this is indeed a really great feature with a great power. Anyway, I am trying to write a python script that one of its goals is to remove some data libraries, But until now, I was unable to find a way to remove data library or some of its datasets using the API or by direct call to Galaxy's code. I found a old post that claim that this feature is not yet implemented. My questions: 1) Is this has changed since? I mean, is there a way now to clean or remove completely a data library? 2) Is there a way to use Galaxy code to remove a library? Such as a function that can be used in my script to remove this library? Thanks in advance! Liram

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installing tool from ToolShed - Python Error 'too many values to unpack'
by Shantanu Pavgi 30 Apr '12

30 Apr '12

I am getting following "ValueError: too many values to unpack" from Python while trying to install a tool from toll_shed repository. {{{ URL: http://localhost:8080/admin_toolshed/install_repository?tool_shed_url=http%… File '/Users/shantanu/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/Users/shantanu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/Users/shantanu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/Users/shantanu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/Users/shantanu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/Users/shantanu/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/Users/shantanu/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 in decorator return func( self, trans, *args, **kwargs ) File '/Users/shantanu/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 291 in install_repository description, repository_clone_url, changeset_revision = repo_info_tuple ValueError: too many values to unpack }}} I am using galaxy-dist revision 40f1816d6857 on Mac OS 10.7 with Python 2.7. I got the same error on CentOS 5.8 platform with Python 2.6 version for the same galaxy-dist revision. Am I missing anything in the configuration file? Any pointers? Appreciate all the help. -- Thanks, Shantanu

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Cutadapt
by Jennifer Jackson 30 Apr '12

30 Apr '12

Hi Tilahun, This tool is in the Galaxy Tool Shed (http://wiki.g2.bx.psu.edu/Tool%20Shed) so to use for now, use with a local/cloud instance (http://getgalaxy.org) would be the best route: http://galaxy.psu.edu/search/getgalaxy/ search for "cutadapt" I will also forward this to the galaxy-dev list where tools are discussed. Going forward, that would be the best place to make requests. We will open a ticket at bitbucket if the team decides this would be a good fit for the public server. http://wiki.g2.bx.psu.edu/Support#Mailing_Lists Thanks! Jen Galaxy team -------- Original Message -------- Subject: Cutadapt Date: Mon, 30 Apr 2012 13:49:53 -0500 From: Tilahun Abebe <tilahun.abebe(a)uni.edu> To: Jennifer Jackson <jen(a)bx.psu.edu> Hi Jennifer, I want to use cutadapt to trim adapters on Galaxy main. It looks like it is not listed under the tools. Can you add cutadapt to Galaxy? Thanks for your help. Tilahun Abebe University of Northern Iowa

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Re: [galaxy-dev] Galaxy parallel processing
by Nate Coraor 30 Apr '12

30 Apr '12

Hi Kiran, This is a question best directed to the galaxy-dev list, which I have CC'd. On Apr 23, 2012, at 5:23 AM, Kiran Jaycee wrote: > Dear Nate, > > Im deploying Galaxy in the cluster environment with 8 nodes and 96 cores. Im particularly interested in running NGS tools > like BWA, BOWTIE etc in the cluster with Torque PBS. Just wondering if galaxy is capable of parallel processing of data. 1 user running BWA in 10 cores in which 10 instances of BWA in each core parallely processing the mapping of 250 GB of reads data on to the reference genome. > Is this possible? The BWA tool itself supports running multithreaded, see the threads option in the wrapper. Also, Galaxy can split a tool's inputs, run a tool many times, and merge the outputs. I am not sure whether this is possible or implemented with BWA, but I would encourage you to look in to whether this would work for your needs. > I have another issue as well. Im unable to finish FASTQ grooming of the reads of size 250GB even after 2 days of processing. Is there a way to circumvent the grooming step? or any way to make the grooming speed up? Assuming this is on a local server, make sure you have set the config option set_metadata_externally = True. You don't need to run the groomer if your fastq file is valid fastqsanger. --nate > > Your quick response will be really appreciated. > > Thank you > > Regards, > Kiran Jaycee > > Bioinformatician, BINET > ELOGIC Technologies Pvt. Ltd. > #1, 2nd Floor, 100 Ft. Ring Road, > Kathriguppe, Banashankari III Stage, > Bangalore - 560085 > Phone : +91 (0)80 4080 3829 > Website : www.elogic.co.in >

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Re: [galaxy-dev] /bin/sh: samtools: not found-->>WORKAROUND
by Michael Moore 30 Apr '12

30 Apr '12

There is apparently a persistent problem with samtools which normally lives at /usr/bin/samtools. I encountered a similar problem in Python when uploading BAM files. I did not resolve the problem. I hacked for a while on binary.py in a lib/ subdirectory and used os.system to send myself mail describing the effective path at various points, and I added a missing logging.basicConfig() statement and scattered some log.WARNING statements strategically. All this told me nothing. So I made a few symlinks to samtools. The one that got things working was ln -s /usr/bin/samtools /home/galaxy/bin/samtools so--worked around but not resolved. Michael On Tue, Apr 17, 2012 at 12:15 PM, zhengqiu cai <caizhq2005(a)yahoo.com.cn>wrote: > Hi All, > > I submitted a job to convert sam to bam, and the job was running forever > without outputing the result. I then checked the log, and it read: > Traceback (most recent call last): > File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", > line 336, in finish_job > drm_job_state.job_wrapper.finish( stdout, stderr ) > File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/jobs/__init__.py", line > 637, in finish > dataset.set_meta( overwrite = False ) > File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/model/__init__.py", line > 875, in set_meta > return self.datatype.set_meta( self, **kwd ) > File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/datatypes/binary.py", line > 179, in set_meta > raise Exception, "Error Setting BAM Metadata: %s" % stderr > Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found > > It means that the samtools is not in the PATH. I tried to set the PATH in > a couple of methods according the Galaxy documentation: > 1. put the path in the env.sh in the tool directory and symbolink default > to the tool directory, e.g. default -> > =/mnt/galaxyTools/tools/samtools/0.1.18 > 2. put -v PATH=/mnt/galaxyTools/tools/samtools/0.1.18 in ~/.sge_request > 3. put -v PATH=/mnt/galaxyTools/tools/samtools/0.1.18 in /path/sge_request > > none of them worked, and I got the above same problem. > > Then I checked the job log file in the job_working_directory, and it read: > Samtools Version: 0.1.18 (r982:295) > SAM file converted to BAM > > which shows that sge knows the PATH of samtools. To double check it, I > added samtools index to Galaxy, and it worked well. I am very confused why > SGE knows the tool path but cannot run the job correctly. > > The system I am using is ubuntu on EC2. I checked out the code from > galaxy-dist on bitbucket. Other tools such as bwa and bowtie worked well > using the same setting method(put env.sh in the tools directory to set the > tool path) > > Thank you very much for any help or hints. > > Cai > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ >

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