[galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy
Hi all, I want to integrate STAR Aligner v2.2.0c into Galaxy and I was wondering if anyone else is working on this? If nobody is, I would do this. Best regards, Patrick Sorn ___ 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 with Univa Grid Engine (UGE) instead of SGE?
On Tue, Jan 15, 2013 at 7:02 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hello all,
Our local Galaxy server had been running happily under SGE, using
one of the last free releases (not sure exactly which - I could ask).
Due to concerns about long term maintenance, the SysAdmin has
moved us to an SGE compatible setup - Univa Grid Engine (UGE).
However, in at least one respect this is not a drop in replacement,
while other cluster usage appears to be working fine our Galaxy
installation is not, e.g.
...
Debugging this by attempting a manual submission,
$ qsub /mnt/galaxy/galaxy-central/database/pbs/galaxy_331:842.sh
Unable to run job: Colon (':') not allowed in objectname.
Exiting.
Renaming the file to replace the colon with (say) an underscore allows
a manual qsub to work fine with UGE. I've edited Galaxy to avoid the
colons (patch below) but the submission still fails.
Additionally removing the SGE specific settings in universe_wsgi.ini did
allow the job to be submitted I am still having problems. Perhaps I need
to fix all the other filenames too (e.g. stdout, stderr, error code), or do
that
in one go by removing the colon in the job name?
Part of the problem I am facing involves the SGE/UGE specific
arguments I have defined in universe_wsgi.ini (which still work
fine if I use them with qsub manually).
My original settings looked like this,
[galaxy:tool_runners]
ncbi_blastp_wrapper = drmaa://-V -l
hostname=n08-04-008-*|n11-04-048-cortana -pe smp 4/
That worked fine in Galaxy with SGE, and still works fine with UGE using
qsub manually. However, the -pe smp 4 part does not work for queue
submission anymore with UGE. Simplifying to:
[galaxy:tool_runners]
ncbi_blastp_wrapper = drmaa://-V -pe smp 4/
fails:
galaxy.jobs.handler INFO 2013-01-16 11:49:39,603 (346) Job dispatched
galaxy.jobs.runners.drmaa DEBUG 2013-01-16 11:49:40,346 (346)
submitting file /mnt/galaxy/galaxy-central/database/pbs/galaxy_346.sh
galaxy.jobs.runners.drmaa DEBUG 2013-01-16 11:49:40,347 (346) command
is: blastp -version
/mnt/galaxy/galaxy-central/database/tmp/GALAXY_VERSION_STRING_346;
blastp -query /mnt/galaxy/galaxy-central/database/files/000/dataset_344.dat
-db /mnt/shared/cluster/blast/galaxy/oomycete_CDS -task blastp
-evalue 0.001 -out
/mnt/galaxy/galaxy-central/database/files/000/dataset_394.dat
-outfmt 6 -num_threads 8
galaxy.jobs.runners.drmaa DEBUG 2013-01-16 11:49:40,347 (346) spec: -pe smp 4
galaxy.jobs.runners.drmaa ERROR 2013-01-16 11:49:40,351 Uncaught
exception queueing job
Traceback (most recent call last):
File /mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py,
line 146, in run_next
self.queue_job( obj )
File /mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py,
line 235, in queue_job
job_id = self.ds.runJob(jt)
File
/mnt/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py,
line 331, in runJob
_h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate)
File /mnt/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/helpers.py,
line 213, in c
return f(*(args + (error_buffer, sizeof(error_buffer
File /mnt/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py,
line 90, in error_check
raise _ERRORS[code-1](code %s: %s % (code, error_buffer.value))
DeniedByDrmException: code 17: error: no suitable queues
Clearly something is going wrong in passing the option to UGE. Note
this works at the command line:
$ qsub -pe smp 4 /mnt/galaxy/galaxy-central/database/pbs/galaxy_346.sh
Your job 252 (galaxy_346.sh) has been submitted
$ qstat | grep 252
252 0.60500 galaxy_346 galaxy qw01/16/2013 11:50:41
4
If I remove this option, job submission works. Given Galaxy gives UGE the
'native spec' as a string, I don't think this is a Galaxy problem. Rather, it
could be an incompatibility in UGE versus SGE? I can probably workaround
this particular issue - there are other ways to request four processors
and/or a whole cluster node.
So, to recap, I needed to remove any colons in job scripts fixed (crude
patch on previous email), and tweak my SGE/UGE settings in the
universe_wsgi.ini file.
I would also like to see a clear error message for the user when an
DeniedByDrmException is raised during job submission - currently
this is not handled gracefully at all.
I've now had some cluster jobs succeed via Galaxy, but it does not
seem to be as reliable as under SGE. Perhaps there is some heavy
IO on the cluster at the moment which may be confusing things...
Peter
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[galaxy-dev] running parallel workflow fails
Hi, I have a workflow that I can successfully launch on a single FASTQ (the only input of the workflow). I am now trying to start the workflow on 8 different FASTQ files (after demultiplexing) but systematically get this error (local galaxy install): Thx for your help Charles URL: http://manni/galaxy/workflow/run Module paste.exceptions.errormiddleware:143 in __call__ app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:91 in __call__ return self.app( environ, start_response ) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) TypeError: run() takes at least 3 arguments (2 given) ## below is a copy-paste of all variables (if useful): CONTENT_LENGTH '0' HTTP_ACCEPT 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_ENCODING'gzip, deflate' HTTP_ACCEPT_LANGUAGE'en-us' HTTP_AUTHORIZATION 'Basic Z2lyYXJkb3Q6Y3QwMmhlODg=' HTTP_CONNECTION 'Keep-Alive' HTTP_COOKIE 'galaxysession=7df64c2bf0628c5b57afd358adee6e7b2cd6161345bb6b47388e497cbd26f407876c2bed128d9226;wikidb_ngs_Token=1f38fe6b5eb5863596cad189f608835c; wikidb_ngs_UserName=Girardot; wikidb_ngs_UserID=15; wikidb_ngs__session=d9n3qq68n0nl6p6j9t96k5q6m3' HTTP_HOST 'manni' HTTP_REFERER'http://manni/galaxy/workflow/run?id=52d6640a458dfabe' HTTP_REMOTE_USER'girar...@embl.de' HTTP_USER_AGENT 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/534.57.2 (KHTML, like Gecko) Version/5.1.7 Safari/534.57.2' PATH_INFO '/workflow/run' REMOTE_ADDR '10.11.72.108' REQUEST_METHOD 'GET' SCRIPT_NAME '/galaxy' SERVER_NAME 'manni' SERVER_PORT '8080' SERVER_PROTOCOL 'HTTP/1.1' Configuration __file__'/g/funcgen/galaxy/universe_wsgi.combined.ini' admin_users 's...@embl.de,sa...@embl.de,girar...@embl.de,gal...@embl.de' allow_library_path_paste'True' allow_user_dataset_purge'True' allow_user_impersonation'True' api_allow_run_as'gal...@embl.de' cleanup_job 'always' cluster_files_directory '/g/galaxy/galaxy_data/pbs' collect_outputs_from'new_file_path,job_working_directory' cookie_path '/galaxy' database_connection 'postgres://galaxy:galaxy@manni/galaxy_db' database_engine_option_max_overflow '20' database_engine_option_pool_size'10' database_engine_option_server_side_cursors 'True' database_engine_option_strategy 'threadlocal' debug 'True' default_cluster_job_runner 'drmaa://-q gbcs_q -N galaxy_stdjob -l ncpus=1,mem=4gb/' drmaa_external_killjob_script 'scripts/drmaa_external_killer.py' drmaa_external_runjob_script'scripts/drmaa_external_runner.py' enable_api 'True' enable_job_recovery 'True' enable_quotas 'True' enable_tracks 'False' environment_setup_file '/g/funcgen/galaxy/env_setup' error_email_to 'g...@embl.de' external_chown_script 'scripts/external_chown_script.py' file_path '/g/galaxy/galaxy_data/files' here'/g/funcgen/galaxy' id_secret 'all_your_base_are_belong_to_us' job_handlers'runner0' job_manager 'runner0' job_working_directory '/g/galaxy/galaxy_data/job_working_directory' library_import_dir '/home/galaxy/' log_level 'DEBUG' logo_url'http://manni/ngswiki/index.php/Galaxy' new_file_path '/g/galaxy/galaxy_data/tmp' nglims_config_file 'tool-data/nglims.yaml' outputs_to_working_directory'True' qa_url 'http://slyfox.bx.psu.edu:8080/' remote_user_maildomain 'embl.de' require_login 'True' retry_job_output_collection '10' sanitize_all_html 'False' set_metadata_externally 'True' smtp_server 'smtp.embl.de' start_job_runners 'drmaa' static_cache_time '360' static_dir '/g/funcgen/galaxy/static/' static_enabled 'True' static_favicon_dir '/g/funcgen/galaxy/static/favicon.ico' static_images_dir '/g/funcgen/galaxy/static/images' static_robots_txt '/g/funcgen/galaxy/static/robots.txt' static_scripts_dir '/g/funcgen/galaxy/static/scripts/' static_style_dir'/g/funcgen/galaxy/static/june_2007_style/blue' tool_config_file'tool_conf.xml,shed_tool_conf.xml' tool_dependency_dir '/g/funcgen/galaxy/dependencies' tool_path 'tools' track_jobs_in_database 'True' use_interactive 'False' use_nglims 'False' use_remote_user 'True' WSGI Variables application paste.debug.prints.PrintDebugMiddleware object at 0x22dbdf90 paste.cookies (SimpleCookie: galaxysession='7df64c2bf0628c5b57afd358adee6e7b2cd6161345bb6b47388e497cbd26f407876c2bed128d9226'wikidb_ngs_Token='1f38fe6b5eb5863596cad189f608835c'
[galaxy-dev] JAVAscript error after initiating tool
Hi all, For who is interested. Occasionally I get this strange Javascript error, just after clicking 'run' on a tool. ERROR updating hdas from api history contents:e47699a32b93ce7f The tool gets running, but the history panel is not updated. I click 'analyse data' to see the updated history. Cheers, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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] running parallel workflow fails
Hi, Posted this too quick: just realized that the jobs are actually created although I am getting this error. bw C On 16 Jan 2013, at 13:55, Charles Girardot wrote: Hi, I have a workflow that I can successfully launch on a single FASTQ (the only input of the workflow). I am now trying to start the workflow on 8 different FASTQ files (after demultiplexing) but systematically get this error (local galaxy install): Thx for your help Charles URL: http://manni/galaxy/workflow/run Module paste.exceptions.errormiddleware:143 in __call__ app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:91 in __call__ return self.app( environ, start_response ) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) TypeError: run() takes at least 3 arguments (2 given) ## below is a copy-paste of all variables (if useful): CONTENT_LENGTH'0' HTTP_ACCEPT 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_ENCODING 'gzip, deflate' HTTP_ACCEPT_LANGUAGE 'en-us' HTTP_AUTHORIZATION'Basic Z2lyYXJkb3Q6Y3QwMmhlODg=' HTTP_CONNECTION 'Keep-Alive' HTTP_COOKIE 'galaxysession=7df64c2bf0628c5b57afd358adee6e7b2cd6161345bb6b47388e497cbd26f407876c2bed128d9226;wikidb_ngs_Token=1f38fe6b5eb5863596cad189f608835c; wikidb_ngs_UserName=Girardot; wikidb_ngs_UserID=15; wikidb_ngs__session=d9n3qq68n0nl6p6j9t96k5q6m3' HTTP_HOST 'manni' HTTP_REFERER 'http://manni/galaxy/workflow/run?id=52d6640a458dfabe' HTTP_REMOTE_USER 'girar...@embl.de' HTTP_USER_AGENT 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/534.57.2 (KHTML, like Gecko) Version/5.1.7 Safari/534.57.2' PATH_INFO '/workflow/run' REMOTE_ADDR '10.11.72.108' REQUEST_METHOD'GET' SCRIPT_NAME '/galaxy' SERVER_NAME 'manni' SERVER_PORT '8080' SERVER_PROTOCOL 'HTTP/1.1' Configuration __file__ '/g/funcgen/galaxy/universe_wsgi.combined.ini' admin_users 's...@embl.de,sa...@embl.de,girar...@embl.de,gal...@embl.de' allow_library_path_paste 'True' allow_user_dataset_purge 'True' allow_user_impersonation 'True' api_allow_run_as 'gal...@embl.de' cleanup_job 'always' cluster_files_directory '/g/galaxy/galaxy_data/pbs' collect_outputs_from 'new_file_path,job_working_directory' cookie_path '/galaxy' database_connection 'postgres://galaxy:galaxy@manni/galaxy_db' database_engine_option_max_overflow '20' database_engine_option_pool_size '10' database_engine_option_server_side_cursors'True' database_engine_option_strategy 'threadlocal' debug 'True' default_cluster_job_runner'drmaa://-q gbcs_q -N galaxy_stdjob -l ncpus=1,mem=4gb/' drmaa_external_killjob_script 'scripts/drmaa_external_killer.py' drmaa_external_runjob_script 'scripts/drmaa_external_runner.py' enable_api'True' enable_job_recovery 'True' enable_quotas 'True' enable_tracks 'False' environment_setup_file'/g/funcgen/galaxy/env_setup' error_email_to'g...@embl.de' external_chown_script 'scripts/external_chown_script.py' file_path '/g/galaxy/galaxy_data/files' here '/g/funcgen/galaxy' id_secret 'all_your_base_are_belong_to_us' job_handlers 'runner0' job_manager 'runner0' job_working_directory '/g/galaxy/galaxy_data/job_working_directory' library_import_dir'/home/galaxy/' log_level 'DEBUG' logo_url 'http://manni/ngswiki/index.php/Galaxy' new_file_path '/g/galaxy/galaxy_data/tmp' nglims_config_file'tool-data/nglims.yaml' outputs_to_working_directory 'True' qa_url'http://slyfox.bx.psu.edu:8080/' remote_user_maildomain'embl.de' require_login 'True' retry_job_output_collection '10' sanitize_all_html 'False' set_metadata_externally 'True' smtp_server 'smtp.embl.de' start_job_runners 'drmaa' static_cache_time '360' static_dir'/g/funcgen/galaxy/static/' static_enabled'True' static_favicon_dir'/g/funcgen/galaxy/static/favicon.ico' static_images_dir '/g/funcgen/galaxy/static/images' static_robots_txt '/g/funcgen/galaxy/static/robots.txt' static_scripts_dir'/g/funcgen/galaxy/static/scripts/' static_style_dir '/g/funcgen/galaxy/static/june_2007_style/blue' tool_config_file 'tool_conf.xml,shed_tool_conf.xml' tool_dependency_dir '/g/funcgen/galaxy/dependencies' tool_path 'tools' track_jobs_in_database'True' use_interactive 'False' use_nglims'False' use_remote_user 'True' WSGI Variables application
Re: [galaxy-dev] macs error for chipseq data
This is great. For the Galaxy tools, will you be able to submit wrappers to the toolshed? This should make it easier for users to install into their local Galaxy instances. Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, Jan 16, 2013 at 8:38 AM, Quang Trinh quang.tr...@gmail.com wrote: Hi Kathryn, We at the modENCODE DCC ( http://www.modencode.org/ ) have been setting up a suite of 3rd party tools for calling peaks ( i.e., macs2, spp, PeakRanger ) using Galaxy on Amazon Cloud the last little while. Please have a look at the README files in the docs folder on our github at https://github.com/modENCODE-DCC/Galaxy Please give it a try and send us your comments/questions to h...@modencode.org. Thanks, Q On Fri, Jan 11, 2013 at 10:59 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Kathryn, I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility. Thanks! Jen Galaxy team On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote: Hi Jen, Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out. It seems to me that MACS was installed…. What is the issue? Thank you very much, Kathryn On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote: Hi Jennifer, Thanks for the information on MACS tools. Yes, I forgot to mention that I used bowtie mapped files as the input. Thank you very much, Kathryn From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Friday, January 11, 2013 3:48 AM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: [External] Re: [galaxy-user] macs error for chipseq data Hello Kathryn, This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 If you need more help with your local install, directing questions to the galaxy-...@bx.psu.edu mailing list would be best, Thanks! Jen Galaxy team On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: Dear galaxy users, I’ve encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error An error occurred running this job: /bin/sh: macs: not found Anybody can kindly provide some hints? Thanks, Kathryn ___ 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/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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/
Re: [galaxy-dev] Workflows
Neil, .../api/workflows is not a path in the galaxy directory, but a URL that you should access over HTTP. For example, if you login to Galaxy Test, and then access https://test.g2.bx.psu.edu/api/workflows you will get a json dict of all of your workflows, including the workflow id that you are looking for. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Tue, Jan 15, 2013 at 8:52 PM, neil.burd...@csiro.au wrote: Hi Sorry if these questions are obvious but I just don’t know how to find the answers. I’m trying to get one of the API examples to work in http://wiki.galaxyproject.org/Learn/API/Examples . I’ve got my API key but how do I get/find the workflow id (f2db41e1fa331b3e in the examples). I’ve created workflow but don’t know how to access this key. Also in the first example it states galaxy_url/api/workflows However I don’t have the “api/workflows” directory structure in my galaxy-dist, do I need to create this? Thanks Neil ___ 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] macs error for chipseq data
Hi James, Yes, we will be putting everything on toolshed shortly. Arthur ( cc'ed ), my student from OICR, will be taking lead on this. Thanks, Q On Wed, Jan 16, 2013 at 11:06 AM, James Taylor ja...@jamestaylor.org wrote: This is great. For the Galaxy tools, will you be able to submit wrappers to the toolshed? This should make it easier for users to install into their local Galaxy instances. Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, Jan 16, 2013 at 8:38 AM, Quang Trinh quang.tr...@gmail.com wrote: Hi Kathryn, We at the modENCODE DCC ( http://www.modencode.org/ ) have been setting up a suite of 3rd party tools for calling peaks ( i.e., macs2, spp, PeakRanger ) using Galaxy on Amazon Cloud the last little while. Please have a look at the README files in the docs folder on our github at https://github.com/modENCODE-DCC/Galaxy Please give it a try and send us your comments/questions to h...@modencode.org. Thanks, Q On Fri, Jan 11, 2013 at 10:59 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Kathryn, I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility. Thanks! Jen Galaxy team On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote: Hi Jen, Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out. It seems to me that MACS was installed…. What is the issue? Thank you very much, Kathryn On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote: Hi Jennifer, Thanks for the information on MACS tools. Yes, I forgot to mention that I used bowtie mapped files as the input. Thank you very much, Kathryn From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Friday, January 11, 2013 3:48 AM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: [External] Re: [galaxy-user] macs error for chipseq data Hello Kathryn, This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 If you need more help with your local install, directing questions to the galaxy-...@bx.psu.edu mailing list would be best, Thanks! Jen Galaxy team On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: Dear galaxy users, I’ve encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error An error occurred running this job: /bin/sh: macs: not found Anybody can kindly provide some hints? Thanks, Kathryn ___ 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/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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/
Re: [galaxy-dev] JAVAscript error after initiating tool
Hi, Joachim If you have access to your server logs, do you see any log messages containing 'Error in history API' around the time those happen? Is there a situation where this happens more often (or a way to reliably reproduce)? I'm unable to reproduce this locally so far. The error definitely can be handled better on the javascript side, but I'd like to track down the API error as well before I change the javascript. Thanks for the help, C On Wed, Jan 16, 2013 at 7:57 AM, Joachim Jacob joachim.ja...@vib.be wrote: Hi all, For who is interested. Occasionally I get this strange Javascript error, just after clicking 'run' on a tool. ERROR updating hdas from api history contents:e47699a32b93ce7f The tool gets running, but the history panel is not updated. I click 'analyse data' to see the updated history. Cheers, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib __**_ 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] Please help with fastx broken pipe
Hi, Fresh new installation of galaxy on a MacPro 12 core Mountain Lion Trying to run fastx_quality_stats: galaxy.jobs.manager DEBUG 2013-01-16 16:03:49,646 (7) Job assigned to handler 'main' galaxy.jobs DEBUG 2013-01-16 16:03:54,759 (7) Working directory for job is: /Users/JS/galaxy-dist/database/job_working_directory/000/7 galaxy.jobs.handler DEBUG 2013-01-16 16:03:54,759 dispatching job 7 to local runner galaxy.jobs.handler INFO 2013-01-16 16:03:54,854 (7) Job dispatched galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:54,919 Local runner: starting job 7 galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:55,198 executing: cat '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' | fastx_quality_stats -Q 33 -o '/Users/JS/galaxy-dist/database/files/000/dataset_7.dat' galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:55,396 execution finished: cat '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' | fastx_quality_stats -Q 33 -o '/Users/JS/galaxy-dist/database/files/000/dataset_7.dat' galaxy.jobs DEBUG 2013-01-16 16:03:55,440 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-01-16 16:03:55,496 setting dataset state to ERROR galaxy.tools DEBUG 2013-01-16 16:03:55,618 Error opening galaxy.json file: [Errno 2] No such file or directory: '/Users/JS/galaxy-dist/database/job_working_directory/000/7/galaxy.json' galaxy.jobs DEBUG 2013-01-16 16:03:55,679 job 7 ended 127.0.0.1 - - [16/Jan/2013:16:03:59 -0400] GET /history HTTP/1.1 200 - http://127.0.0.1:8080/root; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17 Galaxy reports the following error: /bin/sh: fastx_quality_stats: command not found cat: stdout: Broken pipe When run on the cmd line, it runs fine: $ cat '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' | fastx_quality_stats -Q 33 -o '/Users/JS/galaxy-dist/database/files/000/dataset_6.dat' $ more /Users/JS/galaxy-dist/database/files/000/dataset_6.dat column count min max sum meanQ1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count Max_count 1 912999 7 46 3102246933.98 32 35 37 5 25 44 153534 361457 322516 75492 0 912999 2 912999 3 46 2974479732.58 31 34 36 5 24 43 316245 255564 197711 143479 0 912999 Jorge Sepulveda, MD, PhD Associate Director for Laboratory Medicine, Medical Director of Laboratory Informatics, Columbia University Medical Center Associate Professor, Department of Pathology Cell Biology Columbia University College of Physicians and Surgeons PH1590B 622 W 168 St New York, NY 10032 Cell: (917) 862-6050 Office: 212-305-6360 E-mail:jls2...@columbia.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] Error trying to remove trackster visualization in latest galaxy-dist
Hi,Tried to remove a trackster visualization in the latest galaxy-dist and got this error:Error Traceback:View as: Interactive|Text|XML(full)⇝NameError: global name 'util' is not definedURL:http://srv151/visualization/list?f-sharing=Allsort=-update_timef-tags=Alloperation=Deletef-title=Allid=f2db41e1fa331b3eModuleweberror.evalexception.middleware:364inrespond viewapp_iter=self.application(environ,detect_start_response)Modulepaste.debug.prints:98in__call__ viewenviron,self.app)Modulepaste.wsgilib:539inintercept_output viewapp_iter=application(environ,replacement_start_response)Modulepaste.recursive:80in__call__ viewreturnself.application(environ,start_response)Modulegalaxy.web.framework.middleware.remoteuser:91in__call__ viewreturnself.app(environ,start_response)Modulepaste.httpexceptions:632in__call__ viewreturnself.application(environ,start_response)Modulegalaxy.web.framework.base:160in__call__ viewbody=method(trans,**kwargs)Modulegalaxy.web.framework:94indecorator viewreturnfunc(self,trans,*args,**kwargs)Modulegalaxy.webapps.galaxy.controllers.visualization:320inlist viewids=util.listify(kwargs['id'])NameError: global name 'util' is not definedExtra FeaturesDisplay the lines of code near each part of the tracebackShow a debug prompt to allow you to directly debug the code at the tracebackRe-GET Page___ 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/
