Re: [galaxy-dev] Installing Galaxy EC2
Hi Daniel,
Make also sure you use correct firewall settings ('security groups') in
EC2. They are described the Galaxy wiki
(http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted?highlight=%28security%29|%28group%29),
but there are some small differences with the setting applied by
CloudLaunch
(http://dev.list.galaxyproject.org/Cloudman-missing-security-rules-in-wiki-page-td4659826.html#a4659902)
Set by CloudLaunch (during my latest launch):
Ports ProtocolSource CloudMan
1-65535 tcp sg-61ba790a
*1-65535 udp sg-61ba790a *
*-1 icmpsg-61ba790a *
20-21 tcp 0.0.0.0/0 http://0.0.0.0/0
22 tcp 0.0.0.0/0 http://0.0.0.0/0
80 tcp 0.0.0.0/0 http://0.0.0.0/0
3-30100 tcp 0.0.0.0/0 http://0.0.0.0/0
42284 tcp 0.0.0.0/0 http://0.0.0.0/0
Cheers,
Joachim
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 06/10/2013 10:54 PM, Daniel Blankenberg wrote:
Hi Daniel,
This should work fine. You'll need to make sure that you have the host
setting in your universe_wsgi.ini like:
host = 0.0.0.0
and that the port 8080 is open/accessible in the security group
settings for the instance in AWS.
Thanks for using Galaxy,
Dan
On Jun 10, 2013, at 4:42 PM, Daniel Gorelik wrote:
Hello all,
I have a question: does anyone know if it is possible to install
Galaxy on an EC2 instance as you would on a local machine, not using
CloudMan, and then view it in the web browser by going to
public_ip:8080? I have been trying and it has not been working for me.
Thanks so much!
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Re: [galaxy-dev] GATK
Hello Linda, Thanks for your suggestions. i removed the line from xml file but now i am getting different error. # ERROR -- # ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): # ERROR The invalid arguments or inputs must be corrected before the GATK can proceed # ERROR Please do not post this error to the GATK forum # ERROR # ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. # ERROR Visit our website and forum for extensive documentation and answers to # ERROR commonly asked questions http://www.broadinstitute.org/gatk # ERROR # ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-sPZtN_) does not exist. # ERROR -- I mentioned the path for human genome fasta file in .loc file , but again i am getting same error. I am using GATK latest (GenomeAnalysisTK-2.5-2-gf57256b) version. your suggestions are very much appericiated.. Thanks Sridhar On Thu, Jun 6, 2013 at 5:23 PM, Linda Cham lc...@us.ibm.com wrote: Hi Sridhar, About the error, you need to request a key from GATK http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest See under How to obtain and use a GATK key Or by pass it by removing the -et NO_ET line from the xml files. [image: Inactive hide details for sridhar srinivasan ---06/06/2013 06:30:48 AM---Dear Developers, I am running GATK for first time. In]sridhar srinivasan ---06/06/2013 06:30:48 AM---Dear Developers, I am running GATK for first time. In galaxy i use Unified Genotyper. I am From: sridhar srinivasan sridhar2bioi...@gmail.com To: Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 06/06/2013 06:30 AM Subject: [galaxy-dev] GATK Sent by: galaxy-dev-boun...@lists.bx.psu.edu -- Dear Developers, I am running GATK for first time. In galaxy i use Unified Genotyper. I am getting error as below mentioned. # ERROR -- # ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): # ERROR The invalid arguments or inputs must be corrected before the GATK can proceed # ERROR Please do not post this error to the GATK forum # ERROR # ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. # ERROR Visit our website and forum for extensive documentation and answers to # ERROR commonly asked questions *http://www.broadinstitute.org/gatk*http://www.broadinstitute.org/gatk # ERROR # ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see * http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest *http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest for more information and instructions on how to obtain a key. # ERROR -- also suggest me about the Rod file for dbSNP. Thanks Sridhar___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ graycol.gif___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Failing test in tool shed not shown
Hi, my augustus repository is shown under the summary page Latest revision: failing tool tests but I could not see any failing test in the repository. http://testtoolshed.g2.bx.psu.edu/view/bgruening/augustus Cheers, Björn ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Failing test in tool shed not shown
On Tue, Jun 11, 2013 at 9:18 AM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi, my augustus repository is shown under the summary page Latest revision: failing tool tests but I could not see any failing test in the repository. http://testtoolshed.g2.bx.psu.edu/view/bgruening/augustus Cheers, Björn This sounds like the problem I've been having with missing test results. What is interesting is I can see the augustus failure, which does seem to support this being at least partly a caching problem. Test failure below for your reference. Regards, Peter -- Tool test results Automated test environment *Time tested:* ~ 10 hours ago *System:* Linux 3.5.0-21-generic * Architecture:* x86_64 *Python version:* 2.7.3 *Galaxy revision:*9982:8d96629131b0 *Galaxy database version:* 115 *Tool shed revision:* 9981:88873eed0092 *Tool shed database version:* 19 *Tool shed mercurial version:* 2.2.3 Tests that failed *Tool id:* augustus *Tool version:* augustus *Test:* test_tool_00 ( functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3 ) *Stderr:* *Traceback:* Traceback (most recent call last): File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 855, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 4 different than expected, difference (using diff): ( /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsrW4Omf/ testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/bcfe8e0731f8/augustus/test-data/human_augustus_utr-on.gtfv. /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpsx_ZEI/tmpsxWN7Ahuman_augustus_utr-on.gtf ) --- local_file +++ history_data @@ -1,80 +1,35 @@ -# This output was generated with AUGUSTUS (version 2.7). -# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.sta...@uni-greifswald.de) -# and Oliver Keller (kel...@cs.uni-goettingen.de). -# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), -# Using native and syntenically mapped cDNA alignments to improve de novo gene finding -# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 -# No extrinsic information on sequences given. -# Initialising the parameters ... -# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl -# Looks like ./examples/example.fa is in fasta format. -# We have hints for 0 sequences and for 0 of the sequences in the input set. -# -# - prediction on sequence number 1 (length = 9453, name = HS04636) - -# -# Constraints/Hints: -# (none) -# Predicted genes for sequence number 1 on both strands -# start gene g1 -HS04636 AUGUSTUS gene 836 8857 1 + . g1 -HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1 -HS04636 AUGUSTUS tss 836 836 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 836 1017 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id g1.t1; gene_id g1;*Tool id:* augustus *Tool version:* augustus *Test:* test_tool_01 ( functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3 ) *Stderr:* *Traceback:* Traceback (most recent call last): File
Re: [galaxy-dev] Failing test in tool shed not shown
Hi Peter, Indeed a caching issue. Any chance we can improve that output? The diff is not really helpful. Thannks, Björn On Tue, Jun 11, 2013 at 9:18 AM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi, my augustus repository is shown under the summary page Latest revision: failing tool tests but I could not see any failing test in the repository. http://testtoolshed.g2.bx.psu.edu/view/bgruening/augustus Cheers, Björn This sounds like the problem I've been having with missing test results. What is interesting is I can see the augustus failure, which does seem to support this being at least partly a caching problem. Test failure below for your reference. Regards, Peter -- Tool test results Automated test environment Time tested: ~ 10 hours ago System: Linux 3.5.0-21-generic Architecture: x86_64 Python version: 2.7.3 Galaxy revision: 9982:8d96629131b0 Galaxy database version: 115 Tool shed revision: 9981:88873eed0092 Tool shed database version: 19 Tool shed mercurial version: 2.2.3 Tests that failed Tool id: augustus Tool version: augustus Test: test_tool_00 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3) Stderr: Traceback: Traceback (most recent call last): File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 855, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 4 different than expected, difference (using diff): ( /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsrW4Omf/testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/bcfe8e0731f8/augustus/test-data/human_augustus_utr-on.gtf v. /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpsx_ZEI/tmpsxWN7Ahuman_augustus_utr-on.gtf ) --- local_file +++ history_data @@ -1,80 +1,35 @@ -# This output was generated with AUGUSTUS (version 2.7). -# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.sta...@uni-greifswald.de) -# and Oliver Keller (kel...@cs.uni-goettingen.de). -# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), -# Using native and syntenically mapped cDNA alignments to improve de novo gene finding -# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 -# No extrinsic information on sequences given. -# Initialising the parameters ... -# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl -# Looks like ./examples/example.fa is in fasta format. -# We have hints for 0 sequences and for 0 of the sequences in the input set. -# -# - prediction on sequence number 1 (length = 9453, name = HS04636) - -# -# Constraints/Hints: -# (none) -# Predicted genes for sequence number 1 on both strands -# start gene g1 -HS04636 AUGUSTUS gene 836 8857 1 + . g1 -HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1 -HS04636 AUGUSTUS tss 836 836 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 836 1017 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id g1.t1; gene_id g1; Tool id: augustus
Re: [galaxy-dev] Failing test in tool shed not shown
Hi, is every test shown, also if it runs successfully? I'm just wondering because there is no installation test shown. And the diff (is it truncated after X lines?) looks like the entire output is missing. Ciao, Björn On Tue, Jun 11, 2013 at 9:18 AM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi, my augustus repository is shown under the summary page Latest revision: failing tool tests but I could not see any failing test in the repository. http://testtoolshed.g2.bx.psu.edu/view/bgruening/augustus Cheers, Björn This sounds like the problem I've been having with missing test results. What is interesting is I can see the augustus failure, which does seem to support this being at least partly a caching problem. Test failure below for your reference. Regards, Peter -- Tool test results Automated test environment Time tested: ~ 10 hours ago System: Linux 3.5.0-21-generic Architecture: x86_64 Python version: 2.7.3 Galaxy revision: 9982:8d96629131b0 Galaxy database version: 115 Tool shed revision: 9981:88873eed0092 Tool shed database version: 19 Tool shed mercurial version: 2.2.3 Tests that failed Tool id: augustus Tool version: augustus Test: test_tool_00 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/0.3) Stderr: Traceback: Traceback (most recent call last): File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 102, in do_it self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id ) File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 855, in verify_dataset_correctness raise AssertionError( errmsg ) AssertionError: History item 4 different than expected, difference (using diff): ( /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsrW4Omf/testtoolshed.g2.bx.psu.edu/repos/bgruening/augustus/bcfe8e0731f8/augustus/test-data/human_augustus_utr-on.gtf v. /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpsx_ZEI/tmpsxWN7Ahuman_augustus_utr-on.gtf ) --- local_file +++ history_data @@ -1,80 +1,35 @@ -# This output was generated with AUGUSTUS (version 2.7). -# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.sta...@uni-greifswald.de) -# and Oliver Keller (kel...@cs.uni-goettingen.de). -# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), -# Using native and syntenically mapped cDNA alignments to improve de novo gene finding -# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 -# No extrinsic information on sequences given. -# Initialising the parameters ... -# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl -# Looks like ./examples/example.fa is in fasta format. -# We have hints for 0 sequences and for 0 of the sequences in the input set. -# -# - prediction on sequence number 1 (length = 9453, name = HS04636) - -# -# Constraints/Hints: -# (none) -# Predicted genes for sequence number 1 on both strands -# start gene g1 -HS04636 AUGUSTUS gene 836 8857 1 + . g1 -HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1 -HS04636 AUGUSTUS tss 836 836 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 836 1017 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id g1.t1; gene_id g1; -HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id g1.t1;
[galaxy-dev] Galaxy job will stay in waiting under DRMAA runner until manually trigger a command line submission
Hi. Running standalone Galaxy stable_2013.06.03 version on RH6.2 with postgresl db with GPFS filesystem. Setup via the directions in http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster to run all jobs through the LSF DRMAA runner. job_conf.xml: job_conf plugins plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner workers=4/ /plugins handlers handler id=main/ /handlers destinations default=lsf destination id=lsf runner=drmaa/ /destinations /job_conf Scheduler and Galaxy were started. Submit a FASTQ groomer job on a FASTQ file under Galaxy. The groomer job in History will stay in GREY Job is waiting to run state until one physically go onto the node and submits a command line job through the scheduler. Once that command line job (e.g. sleep 5) is submitted then the groomer job will show up in the scheduler's job queue and galaxy's HISTORY will now show it as running. I can submit another groomer job after this and it will show up as running. At times, one will see this type of scenario again where one has to manually start a job under the scheduler on the command line to trigger the galaxy's jobs to start running under the scheduler. Is there some setup I am missing in the job_conf.xml above or a flag not set in universe_wsgi.ini? Searching the Galaxy web, I had read that one can set the track_jobs_in_database=True to trigger it to look in memory or database. But that didn't work either. Wonder if anyone seen this type of issue with any runners and have any suggestions on how to debug and fix this. Thanks. Linda___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Toolshed tool doesn't exist error after installation from toolshed
Hi Simon,
I just installe dour fasta_stats repository form the test tool shed and
successfully executed your fast statistics tool, so I am not able to reproduce
this behavior. There must be a configuration problem in your local Galaxy
instance that is resulting in this behavior, but I cannot tell you what it is.
The problem seems to be that your fasta statistics tool is not properly loaded
into your Galaxy tool box, so your paster log should show an exception when
attempting to load the tool after the repository is installed. Here's what my
paster log shows, what does yours show?
Thanks,
Greg Von Kuster
127.0.0.1 - - [11/Jun/2013:08:52:49 -0400] GET
/admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftesttoolshed.g2.bx.psu.edu%2F
HTTP/1.1 302 - http://localhost:8763/admin_toolshed/browse_tool_sheds;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:21.0) Gecko/20100101
Firefox/21.0
127.0.0.1 - - [11/Jun/2013:08:53:15 -0400] GET
/admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/repository_ids=ea3d74feddb3e781changeset_revisions=3eca3cb79e74
HTTP/1.1 200 -
http://testtoolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=ea3d74feddb3e781changeset_revision=3eca3cb79e74;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:21.0) Gecko/20100101
Firefox/21.0
tool_shed.util.tool_util DEBUG 2013-06-11 08:53:20,794 Loading new tool panel
section: fasta
tool_shed.util.shed_util_common DEBUG 2013-06-11 08:53:20,794 Adding new row
(or updating an existing row) for repository 'fasta_stats' in the
tool_shed_repository table.
tool_shed.util.tool_util DEBUG 2013-06-11 08:53:20,835 Appending to tool panel
section: fasta
127.0.0.1 - - [11/Jun/2013:08:53:20 -0400] POST
/admin_toolshed/prepare_for_install?includes_tools_for_display_in_tool_panel=Trueencoded_repo_info_dicts=7f7b0676b166777988637e98c4b4cf254cac31b0%3A7b2266617374615f7374617473223a205b2250726f647563652062617369632073746174697374696373206f6e20612066617374612f6d756c746966617374612066696c65222c2022687474703a2f2f74657374746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f73696d6f6e2d676c61646d616e2f66617374615f7374617473222c2022336563613363623739653734222c202231222c202273696d6f6e2d676c61646d616e222c207b7d2c207b7d5d7dincludes_tools=Truetool_shed_url=http%3A%2F%2Ftesttoolshed.g2.bx.psu.edu%2Fincludes_tool_dependencies=False
HTTP/1.1 200 -
http://localhost:8763/admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/repository_ids=ea3d74feddb3e781changeset_revisions=3eca3cb79e74;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:21.0) Gecko/20100101
Firefox/21.0
/Users/gvk/workspace/galaxy-central/lib/tool_shed/util/xml_util.py:90:
FutureWarning: The behavior of this method will change in future versions. Use
specific 'len(elem)' or 'elem is not None' test instead.
if elem:
galaxy.tools DEBUG 2013-06-11 08:53:21,609 Loaded tool id:
testtoolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0,
version: 1.0.0 into tool panel.
On Jun 11, 2013, at 12:37 AM, Simon Gladman simon.glad...@monash.edu wrote:
Hi all,
Looked for this in the list but couldn't find it. Admittedly I was using
gmail to search the list so I may have missed it - apologies if so.
I have put a very simple tool into a local toolshed (latest version of
toolshed) which just consists of an xml wrapper and a perl script in the
repository. (attached) I want to test it prior to putting it in the main
toolshed..
When I install the tool into my galaxy (latest-stable version) it installs ok.
I then go to run the tool and it loads the interface quite happily but upon
execute it says tool doesn't exist.
I think its looking in the wrong folder on the server for the tool.
In the main galaxy window:
Tool
'galaxy-dev.genome.edu.au:9009/repos/slugger/fasta_stats/fasta-stats/1.0.0'
does not exist, kwd={'tool_state':
u'80025569356339643261396332633035356535356161303366316533393935313439613834366130616239363a3762323235663566373036313637363535663566323233613230333032633230323236343631373436313733363537343232336132303232333233323232376471002e',
'runtool_btn': u'Execute', 'refresh': u'refresh', 'dataset': u'22'}
In the server log:
galaxy.webapps.galaxy.controllers.tool_runner ERROR 2013-06-11 14:23:14,434
index called with tool id
'galaxy-dev.genome.edu.au:9009/repos/slugger/fasta_stats/fasta-stats/1.0.0'
but no such tool exists
128.250.103.244 - - [11/Jun/2013:14:23:14 +1100] POST /tool_runner/index
HTTP/1.1 200 -
https://galaxy-vbc-test.monash.edu/tool_runner?tool_id=galaxy-dev.genome.edu.au%3A9009/repos/slugger/fasta_stats/fasta-stats/1.0.0;
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/27.0.1453.110 Safari/537.36
The tool is installed in (via the toolshed install process):
shed_tools/galaxy-dev.genome.edu.au/repos/slugger/fasta_stats/94469f4c8a55/fasta_stats
Any ideas?
Cheers,
Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails
Thanks Dannon. I am going with postgres for now while mysql is being fixed. Regards, Linda From: Dannon Baker dannon.ba...@gmail.com To: Linda Cham/Poughkeepsie/IBM@IBMUS Cc: Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de, Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 06/06/2013 04:41 PM Subject:Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails Hi Linda, Sorry I wasn't clear before. The fix for that first issue is in galaxy-central's stable branch, which will be migrated to galaxy-dist probably sometime next week. You can always pull directly from -central though, using 'hg pull -u -b stable http://bitbucket.org/galaxy/galaxy-central/' That said, this doesn't resolve the mysql index issues, which I'm currently working on. I hope to have a fix for them available soon, though. -Dannon On Wed, Jun 5, 2013 at 4:47 PM, Linda Cham lc...@us.ibm.com wrote: Hi Bjorn, Currently seen $ hg tip changeset: 9850:cea3ddf6cdda branch: stable tag: tip user: Nate Coraor n...@bx.psu.edu date: Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 Removed galaxy-dist directory and rerun the hg clone command. $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable destination directory: galaxy-dist requesting all changes adding changesets adding manifests adding file changes added 9851 changesets with 36400 changes to 7175 files updating to branch stable 4132 files updated, 0 files merged, 0 files removed, 0 files unresolved $ cd galaxy-dist $ hg heads changeset: 9850:cea3ddf6cdda branch: stable tag: tip user: Nate Coraor n...@bx.psu.edu date: Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 $ hg pull ; hg update stable pulling from https://bitbucket.org/galaxy/galaxy-dist searching for changes no changes found 0 files updated, 0 files merged, 0 files removed, 0 files unresolved Check the script/manage_db.py: from galaxy import eggs - No decorator line eggs.require( Tempita ) eggs.require( SQLAlchemy ) eggs.require( sqlalchemy_migrate ) $ hg update tip 0 files updated, 0 files merged, 0 files removed, 0 files unresolved $ hg heads changeset: 9850:cea3ddf6cdda branch: stable tag: tip user: Nate Coraor n...@bx.psu.edu date: Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 $ hg update default 82 files updated, 0 files merged, 2 files removed, 0 files unresolved $ hg heads changeset: 9850:cea3ddf6cdda branch: stable tag: tip user: Nate Coraor n...@bx.psu.edu date: Mon Jun 03 16:17:31 2013 -0400 summary: Update tag for stable_2013.06.03 script/manage_db.py still the same as above. Inactive hide details for Björn Grüning ---06/05/2013 04:30:09 PM---Hi Linda, Hi Dannon,Björn Grüning ---06/05/2013 04:30:09 PM---Hi Linda, Hi Dannon, From: Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de To: Linda Cham/Poughkeepsie/IBM@IBMUS Cc: Dannon Baker dannon.ba...@gmail.com, Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 06/05/2013 04:30 PM Subject: Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails Hi Linda, Hi Dannon, Thanks. I tried to do the hg pull and update and hg tip but I do not see the changes in my working directory. So I added the one liner eggs.require( decorator ) to scripts/manage_db.py. Ran the sh manage_db.sh upgrade and get this error: that is really strange. Can you show us what the output of hg tip is? Do you mind to start with a fresh checkout and that particular change? Thanks, Björn inline: graycol.gif___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Installing Galaxy EC2
Hello,
Thanks all, but it it turns out my problem was that the line saying to use the
0.0.0.0 host was commented out.. That was stupid..
Thank you,
Daniel
On Jun 11, 2013, at 6:46 AM, Quang Trinh quang.tr...@gmail.com wrote:
Hi Dan and Joachim
You can also try what my students put together, which is based on a config
file and more simple.
https://github.com/modENCODE-DCC/Galaxy/blob/master/docs/README.how.to.launch.Galaxy
Thanks,
Q
On Tue, Jun 11, 2013 at 3:30 AM, Joachim Jacob | VIB | joachim.ja...@vib.be
wrote:
Hi Daniel,
Make also sure you use correct firewall settings ('security groups') in EC2.
They are described the Galaxy wiki
(http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted?highlight=%28security%29|%28group%29),
but there are some small differences with the setting applied by CloudLaunch
(http://dev.list.galaxyproject.org/Cloudman-missing-security-rules-in-wiki-page-td4659826.html#a4659902)
Set by CloudLaunch (during my latest launch):
Ports ProtocolSource CloudMan
1-65535 tcp sg-61ba790a
*1-65535 udp sg-61ba790a *
*-1 icmpsg-61ba790a *
20-21 tcp 0.0.0.0/0 http://0.0.0.0/0
22 tcp 0.0.0.0/0 http://0.0.0.0/0
80 tcp 0.0.0.0/0 http://0.0.0.0/0
3-30100 tcp 0.0.0.0/0 http://0.0.0.0/0
42284 tcp 0.0.0.0/0 http://0.0.0.0/0
Cheers,
Joachim
Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team
On 06/10/2013 10:54 PM, Daniel Blankenberg wrote:
Hi Daniel,
This should work fine. You'll need to make sure that you have the host
setting in your universe_wsgi.ini like:
host = 0.0.0.0
and that the port 8080 is open/accessible in the security group settings for
the instance in AWS.
Thanks for using Galaxy,
Dan
On Jun 10, 2013, at 4:42 PM, Daniel Gorelik wrote:
Hello all,
I have a question: does anyone know if it is possible to install Galaxy on an
EC2 instance as you would on a local machine, not using CloudMan, and then
view it in the web browser by going to public_ip:8080? I have been trying and
it has not been working for me.
Thanks so much!
___
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and other Galaxy lists, please use the interface at:
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___
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and other Galaxy lists, please use the interface at:
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___
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[galaxy-dev] Trackster error: not able to find the chrom len file
Dear all, I updated to the latest Galaxy stable code, and updated the datatypes_conf.xml. Trackster displays an error after opening a saved view: *** Error: The requested genome file (/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not be opened. Exiting! sort: write failed: standard output: Broken pipe sort: write error Couldn't open /home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len , No such file or directory *** In my universe_wsgi.ini I point to the correct directory where I keep my chrom len files. # Directory where chrom len files are kept, currently mainly used by trackster len_file_path = /mnt/referencedata/trackster Thanks for any advice, Cheers, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] problems with exporting or importing data
Hi. I have uploaded fasta files on the main galaxy server through my FileZilla program. In want to transfer them to the Galaxy at the Huttenhower Lab (see http://huttenhower.org/galaxy/root) page and to do that go to history list when I am logged in at both locations and I select 'Import a History from an archive'. I paste the url address from the main galaxy server (where my archive is located) and select submit. Then I waited for 2 days and nothing was transferred? I am clearly doing something wrong and would really like you input asap. Thank you very much!! Best regards, Anna Edlund My user name is aedl...@jcvi.orgmailto:aedl...@jcvi.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool Shed test framework breaking where run_functional_tests.sh works
Hi, I also have that error in the latest toolshed: AssertionError: Attempting to set field 'topology' to value '['-c']' in form 'tool_form' threw exception: multiple matches to value/label c in list control control: SelectControl(topology=[-c, -l]) If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the test tag set. http://testtoolshed.g2.bx.psu.edu/view/bgruening/trna_prediction Any hint on how to resolve that, or is it a recent regression? Cheers, Björn On Thu, May 9, 2013 at 10:49 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Dave, As you hoped, these test now shows up on the tool page (as expected they are test failures - apparently my install script isn't quite right yet): ... This one is more interesting, and appears to be a problem with the test framework (both tests pass locally via run_functional_tests.sh): http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9 Functional test results for changeset revision 16a1a5ae98e9 of seq_rename 0 tests passed, 2 tests failed, 0 tests missing test components. I'll raise that on a new thread, Here's the output from the (Test) Tool Shed where the tests fail: Tests that failed Tool id: seq_rename Tool version: seq_rename Test: test_tool_00 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3) Stderr: Traceback: Traceback (most recent call last): File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 1320, in run_tool self.submit_form( **kwd ) File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 1270, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['2']' in form 'tool_form' threw exception: cannot find value/label 2 in list control control: SelectControl(new_column=[1]) If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the test tag set. Tool id: seq_rename Tool version: seq_rename Test: test_tool_01 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3) Stderr: Traceback: Traceback (most recent call last): File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 1320, in run_tool self.submit_form( **kwd ) File /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 1270, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label c2 in list control control: SelectControl(new_column=[1]) If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the test tag set. Both tests fail with the following assertion: AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label c2 in list control control: SelectControl(new_column=[1]) If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the test tag set. Both tests pass on my development machine run via: $ ./run_functional_tests.sh -id seq_rename The two tests are defined as follows - identical bar the style used for the column arguments - I was wondering if the Tool Shed testing was stricter about numeric column names, but that does not seem to be relevant: tests test param name=input_file
Re: [galaxy-dev] Fwd: Failed runtime validation of To
This message should be associated with a particular step in the workflow. If you can tell us what tool it is that will help to diagnose. The message means that a parameter that could not be checked until the workflow ran had an invalid value. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Mon, Jun 10, 2013 at 5:19 PM, Sameer Dixit samwise.tec...@gmail.com wrote: Hey all, I've been trying to run a workflow on Galaxy, which basically attempts to establish a correlation between the Chip-Chip, Polymerase binding and Dnase Hypersensitivity data. The input would be these 3 files, I am initially performing a liftover on the Chip-Chip data to convert from hg18 to hg19 and then using the output to establish the correlation. The following error keeps coming up 'Failed runtime validation of To (An invalid option was selected, please verify)' Can anyone please tell me what this might mean? This came up while attempting to run the following tool Traceback (most recent call last): File /galaxy/home/g2main/galaxy_main/lib/galaxy/jobs/runners/__init__.py, line 121, in prepare_job job_wrapper.prepare() File /galaxy/home/g2main/galaxy_main/lib/galaxy/jobs/__init__.py, line 656, in prepare self.tool.handle_unvalidated_param_values( incoming, self.app ) File /galaxy/home/g2main/galaxy_main/lib/galaxy/tools/__init__.py, line 2343, in handle_unvalidated_param_values self.handle_unvalidated_param_values_helper( self.inputs, input_values, app ) File /galaxy/home/g2main/galaxy_main/lib/galaxy/tools/__init__.py, line 2382, in handle_unvalidated_param_values_helper raise LateValidationError( message ) LateValidationError Any assistance would be highly appreciated!! Thanks -Sameer ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] minor SQLAlchemy PostgreSQL issue
The SQLAlchemy postgres dialect was renamed to postgresql. Changing: database_connection = postgres:///... to: database_connection = postgresql:/// in the ini file causes Galaxy (tool_shed in my case) to fail to start as the postgres dialect is mentioned by name a few places in the code. Not a big deal, but I figured I'd report it. -rico ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] How to Install Bowtie?
Hi, Our lab recently installed a local version of Galaxy on Mac OS X 10.8 and can access it at localhost:8080. Now we are trying to install Bowtie version 1 but need help getting it to work. At this point we do not see the tool listed on the left side of the Galaxy menu. Here are the exact steps we followed: 1. create directory /Users/administrator/galaxy-dist/tools_dependencies 2. in universe_wsgi.ini set tool_dependency_dir = tools_dependencies 3. in /etc/paths append /Users/administrator/galaxy-dist/tools_dependencies 4. create tools_dependencies/bowtie/1.0.0/bin 5. create symbolic link tools_dependencies/bowtie/default to directory in step 4 6. download Bowtie, extract it, and copy binaries to tools_dependencies/bowtie/1.0.0/bin Problem: Bowtie is still not appearing in menu on the left side of Galaxy Thanks! ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] minor SQLAlchemy PostgreSQL issue
Even though the dialect name changed, the existing database urls should be compatible (postgres:///...). Did you find this not to be the case? -Dannon On Mon, Jun 10, 2013 at 12:54 PM, Richard Burhans r...@bx.psu.edu wrote: The SQLAlchemy postgres dialect was renamed to postgresql. Changing: database_connection = postgres:///... to: database_connection = postgresql:/// in the ini file causes Galaxy (tool_shed in my case) to fail to start as the postgres dialect is mentioned by name a few places in the code. Not a big deal, but I figured I'd report it. -rico __**_ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/**search/mailinglists/http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Trackster set display mode - Output looks all the same
Hi Linda, 1- Should the "Set display mode" give out different output?Not yet.VCF visualization is new to Galaxy, and mode switching isn't implemented yet. (It will be implemented in the next release.)What you're seeing is the display of individual variants; of course, trying to view so many variants leads to the mismash that you noted.If you zoom in sufficiently, you should see variants without trouble. See the attached screenshot for example. 2- What might be the issue if all I see are the same output or maybe the output displayed is totally incorrect? Might there be some trackster setup that I might be missing for it to draw incorrectly?Everything looks OK so far. FYI, I've created a new page that lists the steps for setting up visualization for a Galaxy instance and updated wiki links/text to point to this page:http://wiki.galaxyproject.org/Visualization%20SetupBest,J.___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] problems with exporting or importing data
Anna, Try following these steps: (1) Make your history accessible (Share or Publish -- Make History Accessible by Link). (2) Export your history again; make sure to wait until you can use the URL to download a .gz file of your history. (3) Try importing it via URL to the Huttenhower Lab Galaxy. Let us know if you have any problems. Best, J. On Jun 10, 2013, at 11:45 AM, Edlund, Anna wrote: Hi. I have uploaded fasta files on the main galaxy server through my FileZilla program. In want to transfer them to the Galaxy at the Huttenhower Lab (see http://huttenhower.org/galaxy/root) page and to do that go to history list when I am logged in at both locations and I select ‘Import a History from an archive’. I paste the url address from the main galaxy server (where my archive is located) and select submit. Then I waited for 2 days and nothing was transferred? I am clearly doing something wrong and would really like you input asap. Thank you very much!! Best regards, Anna Edlund My user name is aedl...@jcvi.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Recently Used Histories
Hello all! I've recently started using Galaxy, and it's a fantastic piece of software. However, I had a question about a possible feature, and any suggestions on how to implement it. My use case involves working with a lot of histories, and I need to jump back and forth between them fairly frequently. However, it's a bit inconvenient to have to click on the Options button on the rightmost pane, Saved Histories in the drop-down menu, and select my history on the main pane. An easier way to switch between histories that were recently used could definitely benefit me, and perhaps other people too. I propose an easily accessible list with links to the 5 most recently visited histories. I took a look at the source, but as I'm unfamiliar with Django and the Galaxy codebase, I thought it might be best to come here for advice. My initial thought was to show the last 5 most recently updated histories underneath the History Lists in the options menu. However, that would probably cause trouble when working when Shared Histories that other people are working on, jumping up to the top of the list whenever anyone edits them. The best solution I could think of was to have some sort of list of the histories visited. When the user selects a history, that history is pushed to the top of the stack, and if there are more than 5 items in the stack, the least recent history is popped off. Ideally, the user wouldn't need to go back to the Saved Histories or Histories Shared With Me grid when working with a few different histories at once. I'm also not sure where the user's state is stored, so I don't know where I would put this variable. I'm also not sure if there's any hooks or anything when selecting a history that I could take advantage of to push it to the top of the user's stack. An issue with this approach is that an item from a history may be open on the main pane, and the user can select another history without going to either grid of histories. This problem doesn't currently occur, because the only way to select a different history is by opening up the history list on the main screen. The main pane needs to be changed to something else upon changing histories, but I don't have any ideas as to what would be best. Perhaps the default Analyze Data screen? Sorry for so many questions! Any answers or suggestions would be much appreciated :) I'm also curious if anyone would benefit from this feature besides myself! ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Trackster set display mode - Output looks all the same
Thank you Jeremy. The new wiki page looks great! Regards, Linda From: Jeremy Goecks jeremy.goe...@emory.edu To: Linda Cham/Poughkeepsie/IBM@IBMUS Cc: galaxy-dev@lists.bx.psu.edu Date: 06/11/2013 12:56 PM Subject:Re: [galaxy-dev] Trackster set display mode - Output looks all the same Hi Linda, 1- Should the Set display mode give out different output? Not yet. VCF visualization is new to Galaxy, and mode switching isn't implemented yet. (It will be implemented in the next release.) What you're seeing is the display of individual variants; of course, trying to view so many variants leads to the mismash that you noted. If you zoom in sufficiently, you should see variants without trouble. See the attached screenshot for example. 2- What might be the issue if all I see are the same output or maybe the output displayed is totally incorrect? Might there be some trackster setup that I might be missing for it to draw incorrectly? Everything looks OK so far. FYI, I've created a new page that lists the steps for setting up visualization for a Galaxy instance and updated wiki links/text to point to this page: http://wiki.galaxyproject.org/Visualization%20Setup Best, J.inline: graycol.gifinline: 1C299461.gif___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Toolshed bug related to readme files
I have run into an issue when trying to reinstall a tool that was originally installed via migration scripts (toolshed version of picard). When I attempt to reinstall (after successfully uninstalling) I get a 500 error. After a bit of poking around, it seems that this URL generates the 500 error: http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picardowner=devteamchangeset_revision=e0232cbac965 Looks like this changeset is relevant: https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696 -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Pasted text in upload.py
Hello, I am trying to understand how the upload.py file works. I have already spent a long time trying to figure this out, but I just cannot at all understand where, for example, a pasted text input is saved. Let's say, for example, I wanted to make any pasted text input all caps. Where would I put .upper? Thank you, Daniel Gorelik ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Recently Used Histories
Hello all! I've recently started using Galaxy, and it's a fantastic piece of software. However, I had a question about a possible feature, and any suggestions on how to implement it. My use case involves working with a lot of histories, and I need to jump back and forth between them fairly frequently. However, it's a bit inconvenient to have to click on the Options button on the rightmost pane, Saved Histories in the drop-down menu, and select my history on the main pane. An easier way to switch between histories that were recently used could definitely benefit me, and perhaps other people too. I propose an easily accessible list with links to the 5 most recently visited histories. I took a look at the source, but as I'm unfamiliar with Django and the Galaxy codebase, I thought it might be best to come here for advice. My initial thought was to show the last 5 most recently updated histories underneath the History Lists in the options menu. However, that would probably cause trouble when working when Shared Histories that other people are working on, jumping up to the top of the list whenever anyone edits them. The best solution I could think of was to have some sort of list of the histories visited. When the user selects a history, that history is pushed to the top of the stack, and if there are more than 5 items in the stack, the least recent history is popped off. Ideally, the user wouldn't need to go back to the Saved Histories or Histories Shared With Me grid when working with a few different histories at once. I'm also not sure where the user's state is stored, so I don't know where I would put this variable. I'm also not sure if there's any hooks or anything when selecting a history that I could take advantage of to push it to the top of the user's stack. An issue with this approach is that an item from a history may be open on the main pane, and the user can select another history without going to either grid of histories. This problem doesn't currently occur, because the only way to select a different history is by opening up the history list on the main screen. The main pane needs to be changed to something else upon changing histories, but I don't have any ideas as to what would be best. Perhaps the default Analyze Data screen? Sorry for so many questions! Any answers or suggestions would be much appreciated :) I'm also curious if anyone would benefit from this feature besides myself! ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] galaxy cuffdiff running too long
Hello, When we run cuffdiff from the command line we get this; [galaxy@q ~]$ /bin/cuffdiff /bin/cuffdiff: /usr/lib64/libz.so.1: no version information available (required by /bin/cuffdiff) cuffdiff v2.0.2 (3522) It looks like we are using a more recent version of cuffdiff than is supported by the galaxy tool wrappers (0.0.5 and 0.0.6). Using the 0.0.5 tool gives empty outputs. Using the 0.0.6 tool results in runs that last for five days without terminating. Has this behavior been seen before? How can we get good outputs to feed into cummeRbund? -Rob ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] galaxy cuffdiff running too long
[galaxy@q ~]$ /bin/cuffdiff /bin/cuffdiff: /usr/lib64/libz.so.1: no version information available (required by /bin/cuffdiff) cuffdiff v2.0.2 (3522) This definitely indicates a problem with your cuffdiff install. Did you build cuffdiff on that system or install in some other way? (very odd to have it installed in /bin). ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Trackster error: not able to find the chrom len file
Trackster displays an error after opening a saved view: *** Error: The requested genome file (/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not be opened. Exiting! sort: write failed: standard output: Broken pipe sort: write error Couldn't open /home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len , No such file or directory *** In my universe_wsgi.ini I point to the correct directory where I keep my chrom len files. # Directory where chrom len files are kept, currently mainly used by trackster len_file_path = /mnt/referencedata/trackster This is a bug: Galaxy wasn't using this setting in converters. I've fixed this in -stable changeset 7105c53: https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a3714bc117118989712a2 Further, I had to remove the 'chr' in the chrom len files to make it work. This is a problem between the UCSC chromosome naming convention (e.g., 'chr1') and the Ensembl naming convention (e.g. '1'). In most cases Galaxy handles this transparently, but the new converters do not. This is something that definitely needs to be implemented. Here's a card so that you can follow the feature's progress: https://trello.com/c/lai0uU9g Best, J.___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Toolshed bug related to readme files
Hi Lance, What version of Galaxy are you running? Is the 500 error coming from your Galaxy server or the tool shed server? Can you send the relevant information from your Galaxy paster log when attempting to reinstall? Thanks, Greg Von Kuster On Jun 11, 2013, at 3:52 PM, Lance Parsons lpars...@princeton.edu wrote: I have run into an issue when trying to reinstall a tool that was originally installed via migration scripts (toolshed version of picard). When I attempt to reinstall (after successfully uninstalling) I get a 500 error. After a bit of poking around, it seems that this URL generates the 500 error: http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picardowner=devteamchangeset_revision=e0232cbac965 Looks like this changeset is relevant: https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696 -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Toolshed bug related to readme files
I'm running the latest stable. The 500 error seems to be coming from the toolshed. Do you also get a 500 error at the toolshed URL in my previous message? There is nothing other than standard info line from the request in my pasted log. I'm not able to get to the log right now, but I'll send it once I get a chance tomorrow. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University Original message From: Greg Von Kuster g...@bx.psu.edu Date: 06/11/2013 10:00 PM (GMT-05:00) To: Lance Parsons lpars...@princeton.edu Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Toolshed bug related to readme files Hi Lance, What version of Galaxy are you running? Is the 500 error coming from your Galaxy server or the tool shed server? Can you send the relevant information from your Galaxy paster log when attempting to reinstall? Thanks, Greg Von Kuster On Jun 11, 2013, at 3:52 PM, Lance Parsons lpars...@princeton.edu wrote: I have run into an issue when trying to reinstall a tool that was originally installed via migration scripts (toolshed version of picard). When I attempt to reinstall (after successfully uninstalling) I get a 500 error. After a bit of poking around, it seems that this URL generates the 500 error: http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picardowner=devteamchangeset_revision=e0232cbac965 Looks like this changeset is relevant: https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696 -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
