Re: [galaxy-dev] Path to tool designation in tool config xml
Thanks, this helps. I was running with an interpreter and I didn't realize I had to had the full path in there. I was expecting that $PATH which contains the directory the script was located in to take care of it. Thanks you very much for the clarification. Timothy ___ 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/
[galaxy-dev] Providing Galaxy tool inputs as an (XML) file?
Hi all, Some of my medium/long term plans for Galaxy involve running one tool which then generates input parameters (and perhaps input files) for another tool. This would be particularly powerful in combination with workflows. One example is phylogenetics where you might have a model selection tool which selects assorted parameters for tree building (e.g. Gamma on or off). General model selection for classifiers might also benefit from such a flow - e.g. Model selection on a subset of the data assessed on a test data set, then running the best model on the full dataset. I can see how I might solve this on a case by case basis, where for each tool which I want to be able to call with a parameter file a wrapper script would be needed, plus the tool would have a top level parameter selection between values from a file, or values entered by the user in the normal way. At least in some niche fields such parameter files already exist - for example the Nexus file format (although many tools which support this as an input format do so in a simplistic way and only look at the alignment or trees, not the commands/settings). However, I'm envisioning a general mechanism for providing (some or all of) the inputs to a Galaxy tool via a file, which for extensibility and consistency with the rest of Galaxy would be in XML. Galaxy would need a nice viewer for this new datatype, which could appear in the history as just another dataset. However, the key new functionality would be on any tool dialogue (if a suitable tool parameter XML file was in the history) would be a new option/button to apply settings from this file to the current form. I'm imagining the new XML would include a list of tool IDs for which it can be used on (e.g. Maximum likelihood model selection might produce settings for both PhyML and RAxML, but these tools might have differently named parameters in their Galaxy tool XML files). Have the Galaxy team been thinking of anything like this already? Thanks, Peter ___ 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/
Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy
Hi, I also faced the same problem. I have a local galaxy and local ucsc genome browser mirror. The galaxy mirror is configured with the require_login equals to True. When I tried to display the data from galaxy to the local ucsc, I encountered the redirected to non-http(s): /root error as well. I have also followed the work around as described in the thread http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-April/002370.html, but I still encounter the redirected to non-http(s): /root error intermittently. Is there a fix or workaround to this problem that works? Thanks for your help. Best regards, Chee Seng, Chan -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor Sent: Tuesday, August 16, 2011 3:49 AM To: Sergei Ryazansky Cc: Galaxy Dev Subject: Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy Sergei Ryazansky wrote: Hi all, I would like to update the issue. I have found the following thread from the galaxy-dev list: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-April/002370.html and according to the suggestion from it I have modified the UCSC_SITES in lib/galaxy/web/framework/__init__.py and 'sites' in lib/galaxy/security/__init__.py. Now these files contatin the url of our local mirror. After these changing the calling of display of bed file in local UCSC Genome Browser results in the following error message: Unrecognized format line 1 of http://dmbcserv.dyndns.org/galaxy/root/display_as?id=436display_app=ucscauthz_method=display_at: You are not allowed to access this dataset. (note: chrom names are case sensitive) You can check this on our public Galaxy mirror: http://dmbcserv.dyndns.org/galaxy. Have you any idea how to fix this? Hi Sergei, It looks like this may be a bug with the external display authorization and the require_login feature. I'll take a look as soon as possible. --nate 2011/7/7 Sergei Ryazansky s.ryazan...@gmail.com Hi Nate, No, our Galaxy server is not behind Apache. Our Galaxy is configured as it is can be used only by registered users, not anonymous. If I disable require_login in universe_wsgi.ini file then displaying of tracks in our UCSC mirror work fine. But enabling this setting results to the mentioned above error. 06.07.2011 22:30, Nate Coraor пишет: Sergei Ryazansky wrote: Hello all, we have the UCSC genome browser mirror as well as Galaxy mirror. The Galaxy has a feature enabling a user to display the data at UCSC genome browser as custom tracks. I have configured the galaxy to display the data to our UCSC browser mirror but it doesn't work properly: after the redirecting to genome browser page the redirected to non-http(s): /root error message is appeared. At the same time displaying Galaxy data at official UCSC works excellent. What are the possible reasons of it? Thank you in advance! Hi Sergei, If your Galaxy server is behind a proxy server serving via https, have you set the following header: RequestHeader set X-URL-SCHEME https Please see the SSL section of the ApacheProxy page for more information: https://bitbucket.org/galaxy/**galaxy-central/wiki/Config/** ApacheProxyhttps://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy --nat ___ 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/ ___ 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/
[galaxy-dev] Tool Shed problems with browse repository files?
Hi all, I've been having a few server errors and other problems browsing files for tool shed repositories, for example clicking to expand a folder sometimes gives a red exclamation icon with the text Load error! (error). Other times it does load but seems to merge several entries into single lines, e.g. clustalw -- rgclustal/ README rgClustal_testout.fasta rgClustalw.xml rgClustal_testin.fasta rgClustal_testout.log Or, clustalomega -- clustalomega/ - clustal-omega-1.0.2/ README test-data/ - hide_stderr.py rgClustalOmega.xml Could someone take a look at this please? Thanks, Peter ___ 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/
Re: [galaxy-dev] value_label tool input param attribute doesn't work as documented
Hi again,
Sorry had to check what exactly was not working, the value_label
attribute appears to not work when trying to reference a label from a
dynamic_options driven input parameter.
regards,
Leandro
On Wed, Aug 24, 2011 at 7:23 PM, Kanwei Li kan...@gmail.com wrote:
Hi Leandro,
I tested this on my instance and the example you gave did give me the
correct string: Human (hg18). Do you still have this problem? If so, can you
provide an example where it still behaves incorrectly?
Thanks,
K
On Thu, Jul 14, 2011 at 4:16 AM, Leandro Hermida
soft...@leandrohermida.com wrote:
Hi,
Looking at the example on the Tool Config Syntax wiki page:
Example
Assume that the tool includes an input parameter named database which is
a select list ( e.g., assume the following inputs ):
Toggle line numbers
1 inputs
2 param format=tabular name=input type=data label=Input
stuff/
3 param type=select name=database label=Database
4 option value=alignseq.locHuman (hg18)/option
5 option value=faseq.locFly (dm3)/option
6 /param
7 /inputs
Assume that the user selects the first option in the $database select
list. Then the following will ensure that the tool produces a tabular data
set whose associated history item has the label Blat on Human (hg18).
Toggle line numbers
1 outputs
2 data format=input name=output label=Blat on
${database.value_label} /
3 /outputs
It shows that .value_label attribute should produce the string in between
the option tags, not the actual value.
Why does this not work? When I use it it produces the value, or am I doing
something wrong?
regards,
Leandro
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Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion)
Whyte, Jeffrey wrote: Nate, For some reason, ~/galaxy-dist wasn't in my PATH. Here is the output when the script is run from the ~/galaxy-dist directory: [~/galaxy-dist] myuserid 03:50 PM python ./scripts/get_platforms.py macosx-10.6-intel-ucs2 [~/galaxy-dist] myuserid 03:50 PM Looks like it is set for Mac OS X 10.6 Snow Leopard instead of 10.7 Lion. (?) This is normal since OS X has binary compatibility with older releases, the Python distributors build for an older platform rather than each individual platform. I see there's now an Intel-only build for 10.6+, I'll work on this ASAP. Thanks, Jeff On Sep 6, 2011, at 10:18 AM, Nate Coraor wrote: Whyte, Jeffrey wrote: Thanks for the information, Nate. I installed Python as you described, and the error I get now is pasted below. I appreciate your help. Jeff [~/galaxy-dist] myuserid 03:06 PM ./run.sh Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched pysam 0.4.2 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e pysam Fetch failed. [~/galaxy-dist] myuserid 03:06 PM Could you report back with the output of: % python ./scripts/get_platforms.py ? Thanks, --nate From: Nate Coraor [n...@bx.psu.edu] Sent: Friday, September 02, 2011 1:16 PM To: Whyte, Jeffrey Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion) Whyte, Jeffrey wrote: Hi, I've been having trouble running a local instance of Galaxy on a Mac Pro after upgrading to OS X 10.7 (Lion). My Python version is 2.7.1 and Mercurial is 1.9.1 for MacOS X 10.7. I don't have any MacPorts installed. The error I see after running the startup script is pasted at the end of this message. Thanks in advance for any help or advice. jjw Hi Jeffrey, We haven't yet gotten our dependencies up to speed on Lion. Could you grab a copy of Python from python.org and use this? It'll install under /Library/Frameworks/Python.framework, just add the correct bin/ directory to the front of your $PATH and start Galaxy as normal. Sorry for the inconvenience, --nate - [~/galaxy-dist] myuserid 10:11 AM ./run.sh Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: decorator (a dependent egg of sqlalchemy-migrate) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 30, in module c.resolve() # Only fetch eggs required by the config File /Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py, line 345, in resolve egg.resolve() File /Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py, line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File /Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py, line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py, line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. [~/galaxy-dist] myuserid 10:12 AM ___ 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/ ___ 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/
Re: [galaxy-dev] Path to tool designation in tool config xml
Timothy Wu wrote: Thanks, this helps. I was running with an interpreter and I didn't realize I had to had the full path in there. I was expecting that $PATH which contains the directory the script was located in to take care of it. Thanks you very much for the clarification. If the script is executable and in your $PATH and has the proper #! line at the top, you don't need 'interpreter='. --nate Timothy ___ 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/ ___ 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/
Re: [galaxy-dev] Tool Shed problems with browse repository files?
Hello Peter, On Sep 7, 2011, at 6:47 AM, Peter Cock wrote: Hi all, I've been having a few server errors and other problems browsing files for tool shed repositories, for example clicking to expand a folder sometimes gives a red exclamation icon with the text Load error! (error). This is a result of memory issues on the server hosting the tool shed. We're in the process of upgrading the hardware, so this issue should go away soon. Other times it does load but seems to merge several entries into single lines, e.g. clustalw -- rgclustal/ README rgClustal_testout.fasta rgClustalw.xml rgClustal_testin.fasta rgClustal_testout.log Or, clustalomega -- clustalomega/ - clustal-omega-1.0.2/ README test-data/ - hide_stderr.py rgClustalOmega.xml This is a due to a recently introduced bug that has now been resolved. Thanks for pointing it out. Could someone take a look at this please? Thanks, Peter ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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/
Re: [galaxy-dev] Installation error
Nate, You were right: I was using Python 2.4; should have checked. I changed the symlink in /opt/galaxy-python to point at a compiled version of Python 2.7. I then ran the run.sh script, only to get the same errors again. I've even tried Python 3.2. Any clues? I run ROCKS 5.3. Thanks! Nikhil On Sep 2, 2011, at 12:43 PM, Nate Coraor wrote: IT Support wrote: Greetings, I attempted to install Galaxy on a ROCKS 5.3 cluster. I checked out Galaxy to a location commonly accessible by all analysis nodes. I then set the path to Python 2.7 like so: export PATH=/opt/galaxy-python/python:$PATH However, executing run.sh gives me the error at the end of this message. The strange thing is that Galaxy runs fine on a CentOS 5.6 virtual machine. Any help would be much appreciated. Thanks! Hi, It looks despite adjusting $PATH, you're still getting Python 2.4. $PATH should point to the directory which contains the `python` binary, could this be: /opt/galaxy-python/python/bin ? --nate - Traceback (most recent call last): File ./scripts/paster.py, line 34, in ? command.run() File /opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py, line 123, in invoke exit_code = runner.run(args) File /opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py, line 218, in run result = self.command() File /opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py, line 276, in command relative_to=base, global_conf=vars) File /opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py, line 311, in loadapp return loadapp( File /opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py, line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File /opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py, line 225, in loadobj return context.create() File /opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py, line 625, in create return self.object_type.invoke(self) File /opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py, line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File /opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/util/fixtypeerror.py, line 57, in fix_call val = callable(*args, **kw) File /opt/galaxy-dist/lib/galaxy/web/buildapp.py, line 90, in app_factory add_controllers( webapp, app ) File /opt/galaxy-dist/lib/galaxy/web/buildapp.py, line 39, in add_controllers module = __import__( module_name ) File /opt/galaxy-dist/lib/galaxy/web/controllers/admin.py, line 310 link=( lambda item: (dict( operation=Manage users and groups, id=item.id, webapp=galaxy ) if not item.default else dict( operation=Change amount, id=item.id, webapp=galaxy )) ), - ___ 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/ ___ 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/
Re: [galaxy-dev] Installation error
Nikhil, As the user who is running galaxy type $which python Something to remember is in $PATH the first folder that points to python wins. I actually use python 2.5.1 and it works perfectly. I also set the user environment ~/bin to search first (beginning of export PATH=~/bin/:/usr/bin/:/usr/local/bin/ ). My symlink to the python 2.5.1 is within bin folder from my home shell. Mykey On 9/7/11 11:17 AM, IT Support supp...@eng.uiowa.edu wrote: Nate, You were right: I was using Python 2.4; should have checked. I changed the symlink in /opt/galaxy-python to point at a compiled version of Python 2.7. I then ran the run.sh script, only to get the same errors again. I've even tried Python 3.2. Any clues? I run ROCKS 5.3. Thanks! Nikhil On Sep 2, 2011, at 12:43 PM, Nate Coraor wrote: IT Support wrote: Greetings, I attempted to install Galaxy on a ROCKS 5.3 cluster. I checked out Galaxy to a location commonly accessible by all analysis nodes. I then set the path to Python 2.7 like so: export PATH=/opt/galaxy-python/python:$PATH However, executing run.sh gives me the error at the end of this message. The strange thing is that Galaxy runs fine on a CentOS 5.6 virtual machine. Any help would be much appreciated. Thanks! Hi, It looks despite adjusting $PATH, you're still getting Python 2.4. $PATH should point to the directory which contains the `python` binary, could this be: /opt/galaxy-python/python/bin ? --nate - Traceback (most recent call last): File ./scripts/paster.py, line 34, in ? command.run() File /opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command. py, line 84, in run invoke(command, command_name, options, args[1:]) File /opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command. py, line 123, in invoke exit_code = runner.run(args) File /opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command. py, line 218, in run result = self.command() File /opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py , line 276, in command relative_to=base, global_conf=vars) File /opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py , line 311, in loadapp return loadapp( File /opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi .py, line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File /opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi .py, line 225, in loadobj return context.create() File /opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi .py, line 625, in create return self.object_type.invoke(self) File /opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi .py, line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File /opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/util/fix typeerror.py, line 57, in fix_call val = callable(*args, **kw) File /opt/galaxy-dist/lib/galaxy/web/buildapp.py, line 90, in app_factory add_controllers( webapp, app ) File /opt/galaxy-dist/lib/galaxy/web/buildapp.py, line 39, in add_controllers module = __import__( module_name ) File /opt/galaxy-dist/lib/galaxy/web/controllers/admin.py, line 310 link=( lambda item: (dict( operation=Manage users and groups, id=item.id, webapp=galaxy ) if not item.default else dict( operation=Change amount, id=item.id, webapp=galaxy )) ), - ___ 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/ ___ 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/ ___ 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/
[galaxy-dev] cuffcompare wrapper
Hi Jeremy, The symlink in the cuffcompare wrapper was causing galaxy to crash because I run as the actual user and have to chmod the job_working directory at the end so Galaxy can clean it up. Turns out is seems like the symlink is not needed. Am I missing something. See below. Your code: for i, arg in enumerate( args ): input_file_name = ./input%i % ( i+1 ) os.symlink( arg, input_file_name ) cmd += %s % input_file_name My code: for i, arg in enumerate( args ): cmd += arg Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: icho...@illumina.commailto:icho...@illumina.com Website: www.illumina.comhttp://www.illumina.com ___ 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/
Re: [galaxy-dev] GATK Unified Genotyper
Hi Daniel,
I have been implementing the GATK unified genotyper and I was having some
issues. Occasionally I would get an error that the Java virtual machine would
not start. I got around that by adding the Xmx3g parameter to the command line.
I also added the -nt 3 because otherwise it's really slow on human data.
--stdout ${output_log}
#for $i, $input_bam in enumerate( $reference_source.input_bams ):
-d -I ${input_bam.input_bam} ${input_bam.input_bam.ext}
gatk_input_${i}
-d ${input_bam.input_bam.metadata.bam_index} bam_index
gatk_input_${i} ##hardcode galaxy ext type as bam_index
#end for
-p 'java -Xmx3g
-jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar
-T UnifiedGenotyper
-o ${output_vcf}
##-o out_vcf.txt
-et NO_ET ##ET no phone home
##-log ${output_log} ##don't use this to log to file, instead directly
capture stdout
#if $reference_source.reference_source_selector != history:
-R ${reference_source.ref_file.fields.path}
#end if
-nt 3
--standard_min_confidence_threshold_for_calling
${standard_min_confidence_threshold_for_calling}
--standard_min_confidence_threshold_for_emitting
${standard_min_confidence_threshold_for_emitting}
Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582
Email: icho...@illumina.commailto:icho...@illumina.com
Website: www.illumina.comhttp://www.illumina.com
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Re: [galaxy-dev] GATK Unified Genotyper
Hi Ilya,
The JVM can be quite a pain when determining the best way to determine max
memory, however the underlying gatk_wrapper.py script was updated last week in
5970:20215fcf6da7 to allow using -Xmx or XX:DefaultMaxRAMFraction. Each of the
GATK tools are currently already set to use 'XX:DefaultMaxRAMFraction' of 2
(half of ram) - future enhancements to the tool running code will allow this to
be set based upon e.g. number of jobs and available ram per node (no time frame
for this).
It does look like num_threads/nt is now available for the UnifiedGenotyper.
Many of the GATK tools list it as an available parameter, but when run will
give an error saying it is not yet implemented (only can determine by trial and
error or reading source code). I've updated the Unified Genotyper to use
--num_threads 4. Thanks!
It might be a good idea to coordinate the changes you are looking into with
GATK with the changes we are approaching. Any other feedback would also be
greatly appreciated.
Thanks for using Galaxy,
Dan
On Sep 7, 2011, at 1:25 PM, Chorny, Ilya wrote:
Hi Daniel,
I have been implementing the GATK unified genotyper and I was having some
issues. Occasionally I would get an error that the Java virtual machine would
not start. I got around that by adding the Xmx3g parameter to the command
line. I also added the –nt 3 because otherwise it’s really slow on human
data.
--stdout ${output_log}
#for $i, $input_bam in enumerate( $reference_source.input_bams ):
-d -I ${input_bam.input_bam} ${input_bam.input_bam.ext}
gatk_input_${i}
-d ${input_bam.input_bam.metadata.bam_index} bam_index
gatk_input_${i} ##hardcode galaxy ext type as bam_index
#end for
-p 'java -Xmx3g
-jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar
-T UnifiedGenotyper
-o ${output_vcf}
##-o out_vcf.txt
-et NO_ET ##ET no phone home
##-log ${output_log} ##don't use this to log to file, instead directly
capture stdout
#if $reference_source.reference_source_selector != history:
-R ${reference_source.ref_file.fields.path}
#end if
-nt 3
--standard_min_confidence_threshold_for_calling
${standard_min_confidence_threshold_for_calling}
--standard_min_confidence_threshold_for_emitting
${standard_min_confidence_threshold_for_emitting}
Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582
Email: icho...@illumina.com
Website: www.illumina.com
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Re: [galaxy-dev] cuffcompare wrapper
Ok, I figured out why you need the symlink. Can you add an unlink after the process completes? i.e for i, arg in enumerate( args ): input_file_name = ./input%i % ( i+1 ) os.unlink(input_file_name) From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Wednesday, September 07, 2011 9:18 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] cuffcompare wrapper Hi Jeremy, The symlink in the cuffcompare wrapper was causing galaxy to crash because I run as the actual user and have to chmod the job_working directory at the end so Galaxy can clean it up. Turns out is seems like the symlink is not needed. Am I missing something. See below. Your code: for i, arg in enumerate( args ): input_file_name = ./input%i % ( i+1 ) os.symlink( arg, input_file_name ) cmd += %s % input_file_name My code: for i, arg in enumerate( args ): cmd += arg Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: icho...@illumina.commailto:icho...@illumina.com Website: www.illumina.comhttp://www.illumina.com ___ 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/
Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion)
On Sep 7, 2011, at 7:54 AM, Nate Coraor wrote: This is normal since OS X has binary compatibility with older releases, the Python distributors build for an older platform rather than each individual platform. I see there's now an Intel-only build for 10.6+, I'll work on this ASAP. if it helps, here are details from 10.7 % /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python -V Python 2.7.1 % file /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7: Mach-O fat file with 2 architectures % /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python scripts/get_platforms.py macosx-10.7-intel-ucs2 % /usr/local/bin/python -V Python 2.7.2 % file /usr/local/Cellar/python/2.7.2/bin/python2.7 /usr/local/Cellar/python/2.7.2/bin/python2.7: Mach-O 64-bit executable % /usr/local/bin/python scripts/get_platforms.py macosx-10.4-x86_64-ucs2 % brew --config HOMEBREW_VERSION: 0.8 HEAD: 8ba7bf8a53dd750943552458daf824e8c424db23 HOMEBREW_PREFIX: /usr/local HOMEBREW_CELLAR: /usr/local/Cellar HOMEBREW_REPOSITORY: /usr/local HOMEBREW_LIBRARY_PATH: /usr/local/Library/Homebrew Hardware: dual-core 64-bit penryn OS X: 10.7.1 Kernel Architecture: x86_64 Ruby: 1.8.7-249 /usr/bin/ruby = /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby Xcode: 4.1 GCC-4.0: N/A GCC-4.2: build 5666 LLVM: build 2335 MacPorts or Fink? false X11 installed? true % uname -rv 11.1.0 Darwin Kernel Version 11.1.0: Tue Jul 26 16:07:11 PDT 2011; root:xnu-1699.22.81~1/RELEASE_X86_64 % uname -p i386 % uname -m x86_64 ___ 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/
Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion)
Trevor Wennblom wrote: On Sep 7, 2011, at 7:54 AM, Nate Coraor wrote: This is normal since OS X has binary compatibility with older releases, the Python distributors build for an older platform rather than each individual platform. I see there's now an Intel-only build for 10.6+, I'll work on this ASAP. if it helps, here are details from 10.7 % /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python -V Python 2.7.1 % file /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7: Mach-O fat file with 2 architectures % /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python scripts/get_platforms.py macosx-10.7-intel-ucs2 Yeah, this will be a new egg. I'm getting access to a Lion machine shortly and can build for this. % /usr/local/bin/python -V Python 2.7.2 % file /usr/local/Cellar/python/2.7.2/bin/python2.7 /usr/local/Cellar/python/2.7.2/bin/python2.7: Mach-O 64-bit executable % /usr/local/bin/python scripts/get_platforms.py macosx-10.4-x86_64-ucs2 Only one architecture. This one you'll be on your own building eggs for. You should be able to with scramble.py, though. % brew --config HOMEBREW_VERSION: 0.8 HEAD: 8ba7bf8a53dd750943552458daf824e8c424db23 HOMEBREW_PREFIX: /usr/local HOMEBREW_CELLAR: /usr/local/Cellar HOMEBREW_REPOSITORY: /usr/local HOMEBREW_LIBRARY_PATH: /usr/local/Library/Homebrew Hardware: dual-core 64-bit penryn OS X: 10.7.1 Kernel Architecture: x86_64 Ruby: 1.8.7-249 /usr/bin/ruby = /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby Xcode: 4.1 GCC-4.0: N/A GCC-4.2: build 5666 LLVM: build 2335 MacPorts or Fink? false X11 installed? true % uname -rv 11.1.0 Darwin Kernel Version 11.1.0: Tue Jul 26 16:07:11 PDT 2011; root:xnu-1699.22.81~1/RELEASE_X86_64 % uname -p i386 % uname -m x86_64 ___ 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/
Re: [galaxy-dev] Tophat non Sanger input
seems unnecessary since illumina switched over to fastqsanger now. http://www.illumina.com/truseq/quality_101/quality_scores.ilmn On Wed, Aug 31, 2011 at 12:45 AM, Stephen Taylor stephen.tay...@imm.ox.ac.uk wrote: Hi, Is there any plans to enhance the tophat wrapper to accept non Sanger fastqs, as for bowtie? https://bitbucket.org/galaxy/**galaxy-central/changeset/**7a9476924dafhttps://bitbucket.org/galaxy/galaxy-central/changeset/7a9476924daf ? Kind regards and thanks, Steve __**_ 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/ ___ 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/
Re: [galaxy-dev] Automatically removing items from history
i'm resurrecting this thread to see if there's any more support for the idea of deleting intermediate files in a workflow. i think this is an important feature to have. oftentimes a workflow creates many intermediate files no one will ever look at. and leaving it up to the user to cleanup their data files is asking too much. there's another ticket regarding allow users to still be able to preview the metadata of deleted workflow history items and together these would go together nicely. On Wed, Jan 26, 2011 at 1:36 PM, Dannon Baker dannonba...@me.com wrote: Marcel, It isn't currently possible to delete datasets from within workflows. If I'm understanding your situation correctly, to simplify the view of a history after running a workflow, you could use the workflow output toggle (the asterisk next to each output in the workflow editor view) and select only the particular outputs you actually want to see. The rest of the outputs are still in the destination history, but hidden from view by default. This won't help you with disk space, though, so you might also want to use the new functionality available for placing the results of a workflow in a new history to accomplish what you want, deleting the previous history that was cluttered with inputs after the workflow has run. Regarding the Galaxy API, you can look at the README file in the scripts/api/ directory of your galaxy installation (also at https://bitbucket.org/galaxy/galaxy-central/src/76c18b38a3b8/scripts/api/README) for a some examples and hints to get you started. More detailed documentation should be available soon though. -Dannon On Jan 20, 2011, at 4:15 AM, Kempenaar, M (med) wrote: Hello, Is it possible to let a tool in a workflow manage the users history? For instance, I have a tool that takes a variable number of user-uploaded CSV files as input and merges them into one file. Before running this tool, the user thus has a number of CSV files in the history which I would like to 'replace' with the single merged file. I was hoping that when I remove a file from disk that it would also be removed from the history, but that only results in a 'The resource could not be found.' error. Alternatively, is it possible to create a composite datafile/history item from uploaded files? In any case, I would like to remove the separately uploaded files from the users history which makes selecting files for the next step(s) easier. (this is a bit of a followup for: http://gmod.827538.n3.nabble.com/Creating-new-datatype-with-variable-number-of-input-files-td2248444.html ) One other question, is there (any) documentation available on the Galaxy API or a set of example files? Thanks for your input! Regards, Marcel. De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev ___ 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/
