[galaxy-dev] where can I find galaxy code documentation?
From: Eli Reuveni Sent: Monday, April 16, 2012 9:13 AM To: 'galaxy-dev@lists.bx.psu.edu' Subject: where can I find galaxy code documentation? Hi, I have a local galaxy instance in my institute and have few basic questions: 1) I need to enable galaxy to upload large files from the local galaxy server without the need to use the ftp or the file upload module, is there an easy way to do it or do I need to write a special code? 2) I need to customize galaxy Python code (i.e., under the ~/galaxy-dist/lib directory). Where can I find documentation of the galaxy Python classes (using wiki or other format) Thanks in advanced, ___ 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] Workflow Tags
Hi dev-list, I have noticed, that when I clone a workflow, the new workflow apparently inherits all tags from all my workflows or something similar. The result is that when ever I clone a workflow the number of tags in the tag list doubles, and thus rapidly grows towards infinity, and there's not much I can do about it - except to avoid cloning workflows, which is a drag. I get this behavior regardless if the workflow I clone from is tagged or not. Has anyone else seen this? Is there a way to remove all tags from a workflow? Shouldn't a given tag be present only once in the tag list pr. workflow? Now I have the same five tags appearing hundreds of times in each tag-list, and they are very hard - if not impossible to get rid of. Kind Regards Frank Sorensen -- Frank Sørensen, B.Sc., Programmer Molecular Diagnostic Laboratory (MDL) Molekylær Medicinsk Afdeling (MOMA) Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N Tlf. +45 7845 5363 ___ 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] Just wanted to say...
I love the improvements you recently made to the web interface layout in galaxy-central, it's really neat! Collapsing the margins and making everything smoother makes the interface really easier to read. Thanks for the hard work, as always, L-A ___ 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] Workflow Tags
On Mon, Apr 16, 2012 at 8:12 AM, Frank Sørensen frank.soren...@ki.au.dk wrote: Hi dev-list, I have noticed, that when I clone a workflow, the new workflow apparently inherits all tags from all my workflows or something similar. The result is that when ever I clone a workflow the number of tags in the tag list doubles, and thus rapidly grows towards infinity, and there's not much I can do about it - except to avoid cloning workflows, which is a drag. I get this behavior regardless if the workflow I clone from is tagged or not. Has anyone else seen this? Is there a way to remove all tags from a workflow? Shouldn't a given tag be present only once in the tag list pr. workflow? Now I have the same five tags appearing hundreds of times in each tag-list, and they are very hard - if not impossible to get rid of. Kind Regards Frank Sorensen Hi Frank, This sounds like the bug Anthonius deBoer reported last month which Dannon has fixed: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-March/009000.html Which release are you running? Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Workflow Tags
Hi Peter, Thanks for the prompt answer. I'm not quite sure which release I'm running. But I'll try to update and see if the problem is solved. Kind Regards Frank Den 16-04-2012 09:54, Peter Cock skrev: On Mon, Apr 16, 2012 at 8:12 AM, Frank Sørensenfrank.soren...@ki.au.dk wrote: Hi dev-list, I have noticed, that when I clone a workflow, the new workflow apparently inherits all tags from all my workflows or something similar. The result is that when ever I clone a workflow the number of tags in the tag list doubles, and thus rapidly grows towards infinity, and there's not much I can do about it - except to avoid cloning workflows, which is a drag. I get this behavior regardless if the workflow I clone from is tagged or not. Has anyone else seen this? Is there a way to remove all tags from a workflow? Shouldn't a given tag be present only once in the tag list pr. workflow? Now I have the same five tags appearing hundreds of times in each tag-list, and they are very hard - if not impossible to get rid of. Kind Regards Frank Sorensen Hi Frank, This sounds like the bug Anthonius deBoer reported last month which Dannon has fixed: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-March/009000.html Which release are you running? Peter -- Frank Sørensen, B.Sc., Programmer Molecular Diagnostic Laboratory (MDL) Molekylær Medicinsk Afdeling (MOMA) Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N Tlf. +45 7845 5363 ___ 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] This link may not be followed from within Galaxy.
Hi, I am getting the error This link may not be followed from within Galaxy. When I try to upload a data file to my local galaxy. I have traced back the error to root.py (RootController class). Could anyone help me with that? Best ___ 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] Issues with local instance of toolshed?
Hi Amanda, I'll need to see your paster log to be able to help on this one. You can view it using tail -f community_webapp.log (without the quotes) from your Galaxy install directory. Can you respond back with the content? Thanks, Greg Von Kuster On Apr 8, 2012, at 1:58 PM, Amanda Zuzolo wrote: Hello all, I've recently been trying to implement a local instance of the tool shed, and have followed the tutorials on the wiki, but when I run sh run_community.sh, it doesn't do anything. I have mercurial installed, so that shouldn't be a problem, and I've used the example community_wsgi.ini and run_community.sh. I can pastebin what I have if it would help. Thank you in advance. -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity ___ 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] problem with ~/lib/galaxy/app.py after code upgrade to March 12, 2012 release ('6799:40f1816d6857')
Hi
We are in the process of migrating our Galaxy servers to the current
March 12, 2012 release ('6799:40f1816d6857').
We have encountered two issues, which I guess are related:
If I restart the server, I get:
galaxy.model.migrate.check INFO 2012-04-16 09:24:50,391 At database
version 93
galaxy.tool_shed.migrate.check DEBUG 2012-04-16 09:24:50,407
MySQL_python egg successfully loaded for mysql dialect
Traceback (most recent call last):
File //galaxy_dist/lib/galaxy/web/buildapp.py, line 82, in
app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File //galaxy_dist/lib/galaxy/app.py, line 37, in __init__
verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
File //galaxy_dist/lib/galaxy/tool_shed/migrate/check.py, line
42, in verify_tools
db_schema = schema.ControlledSchema( engine, migrate_repository )
File
//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 24, in __init__
self._load()
File
//galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 42, in _load
data = list(result)[0]
IndexError: list index out of range
I can 'temporary' fix this by commenting-out line 36 and 37 in
~/lib/galaxy/app.py
36#from galaxy.tool_shed.migrate.check import verify_tools
37#verify_tools( self, db_url, kwargs.get( 'global_conf', {}
).get( '__file__', None ), self.config.database_engine_options )
...well, I don't like this fix, and I wonder if there is a better one?
I have a suspicion, that this is related to problems I encountered
during the database schema upgrade to version 93 for our MySQL database:
at step 90to91 and 91to92 I get the following:
90 - 91...
Migration script to create the tool_version and tool_version_association
tables and drop the tool_id_guid_map table.
0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,719 Creating
tool_version table failed: (OperationalError) (1050, Table
'tool_version' already exists) u'\nCREATE TABLE tool_version (\n\tid
INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME,
\n\tupdate_time DATETIME, \n\ttool_id VARCHAR(255),
\n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN
KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id)\n)\n\n' ()
0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,719 Creating
tool_version table failed: (OperationalError) (1050, Table
'tool_version' already exists) u'\nCREATE TABLE tool_version (\n\tid
INTEGER NOT NULL AUTO_INCREMENT, \n\tcreate_time DATETIME,
\n\tupdate_time DATETIME, \n\ttool_id VARCHAR(255),
\n\ttool_shed_repository_id INTEGER, \n\tPRIMARY KEY (id), \n\t FOREIGN
KEY(tool_shed_repository_id) REFERENCES tool_shed_repository (id)\n)\n\n' ()
0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,720 Creating
tool_version_association table failed: (OperationalError) (1050, Table
'tool_version_association' already exists) u'\nCREATE TABLE
tool_version_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT,
\n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL,
\n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version
(id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n' ()
0091_add_tool_version_tables DEBUG 2012-04-16 08:55:49,720 Creating
tool_version_association table failed: (OperationalError) (1050, Table
'tool_version_association' already exists) u'\nCREATE TABLE
tool_version_association (\n\tid INTEGER NOT NULL AUTO_INCREMENT,
\n\ttool_id INTEGER NOT NULL, \n\tparent_id INTEGER NOT NULL,
\n\tPRIMARY KEY (id), \n\t FOREIGN KEY(tool_id) REFERENCES tool_version
(id), \n\t FOREIGN KEY(parent_id) REFERENCES tool_version (id)\n)\n\n' ()
Added 0 rows to the new tool_version table.
done
91 - 92...
Migration script to create the migrate_tools table.
0092_add_migrate_tools_table DEBUG 2012-04-16 08:55:49,920 Creating
migrate_tools table failed: (OperationalError) (1050, Table
'migrate_tools' already exists) u'\nCREATE TABLE migrate_tools
(\n\trepository_id VARCHAR(255), \n\trepository_path TEXT, \n\tversion
INTEGER\n)\n\n' ()
0092_add_migrate_tools_table DEBUG 2012-04-16 08:55:49,920 Creating
migrate_tools table failed: (OperationalError) (1050, Table
'migrate_tools' already exists) u'\nCREATE TABLE migrate_tools
(\n\trepository_id VARCHAR(255), \n\trepository_path TEXT, \n\tversion
INTEGER\n)\n\n' ()
done
the bizarre thing is, all three tables: 'migrate_tools',
'tool_version_association','tool_version' are present.well, this
explains the error: 'OperationalError 1050, Table 'migrate_tools'
already exists 'but why were the commands executed a second and
third time? - what happened during the first execution?
I can execute the three create statements without problems in a dummy
database on the same MySQl server (Server version:
Re: [galaxy-dev] Workflow import error
Hi Rob, When you import a workflow into a Galaxy instance, the instance must have all tools required by the workflow available in its tool panel. I've only seen this error when the workflow requires a tool that is not available, so can you let us know if this is the case? Thanks, Greg Von Kuster On Apr 16, 2012, at 10:07 AM, Robert Chase wrote: Hi Greg, After I modified the modules.py file that bug went away, but now I'm getting a new error: Module galaxy.web.base.controller:420 in get_stored_workflow_steps view module = module_factory.from_workflow_step( trans, step ) #Check if tool was upgraded step.upgrade_messages = module.check_and_update_state() # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) step.upgrade_messages = module.check_and_update_state() AttributeError: 'NoneType' object has no attribute 'check_and_update_state' -Rob On Mon, Apr 16, 2012 at 9:19 AM, Robert Chase re...@channing.harvard.edu wrote: Thanks Greg, I'll try to merge the change into my version. -Rob On Mon, Apr 16, 2012 at 9:18 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Robert, Thanks for reporting this issue - it has been fixed in change set 7038:1fdcce63a06f, which is currently available only in our central repository. It will be available in the dist in the next update. Greg Von Kuster On Apr 13, 2012, at 5:22 PM, Robert Chase wrote: Hello All, I'm pretty sure I found a bug in the main galaxy distribution. The following code diff shows the introduction of the line tool_version = self.__get_tool_version( trans, tool_id ) but if you look at the function definition containing that line, you see def from_workflow_step( Class, trans, step ): which does not half a self in it. Then we get an error. https://bitbucket.org/galaxy/galaxy-dist/diff/lib/galaxy/workflow/modules.py?diff2=e6464387ed3fdiff1=c60760713d26 -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/ ___ 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] GCC2012 Abstract Submission Deadline is April 16, one week from today.
Hello all, Just a reminder that the abstract submission deadline for the 2012 Galaxy Community Conference (GCC2012) is TODAY. See http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts for details. Thanks, Dave C On Mon, Apr 9, 2012 at 2:03 PM, Dave Clements cleme...@galaxyproject.orgwrote: Hello all, Just a reminder that the abstract submission deadline for the 2012 Galaxy Community Conference (GCC2012) is April 16, one week from today. See http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts for details. Thanks, and hope to see you in Chicago, Dave C On Mon, Feb 13, 2012 at 3:27 PM, Dave Clements cleme...@galaxyproject.org wrote: Hello all, Abstracts http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts are now being accepted for oral presentations at the 2012 Galaxy Community Conference (GCC2012) http://wiki.g2.bx.psu.edu/Events/GCC2012. Submissions on any topics of interest to the Galaxy community are encouraged. Areas of interest include, but are not limited to: - Best practices for local Galaxy installation and management - Integrating tools and/or data sources into the Galaxy framework - Deploying galaxy on different infrastructures - Compelling or novel uses of Galaxy for biomedical analysis See the GCC2011 program http://wiki.g2.bx.psu.edu/Events/GCC2011 for an idea of the breadth of topics that can be covered. Oral presentations will be approximately 15-20 minutes long, including time for question and answer. There will also be an opportunity for lightning talks, which will be solicited at the meeting. The submission deadline is April 16. See the GCC2012 Abstracts http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts page for more details and how to submit. GCC2012 http://wiki.g2.bx.psu.edu/Events/GCC2012 will be held, July 25-27 in Chicago, Illinois, United States. The main meeting will run for two full days http://wiki.g2.bx.psu.edu/Events/GCC2012/Program, and be preceded by a full day of training workshopshttp://wiki.g2.bx.psu.edu/Events/GCC2012/Program. If you are a bioinformatics tool developer, data provider, workflow developer, power bioinformatics user, sequencing or bioinformatics core staff, or a data and analysis archival specialist, then GCC2012 is relevant to you. Registration will open in March. GCC2012 is hosted by the University of Illinois at Chicagohttp://uic.edu/, the University of Illinois at Urbana-Champaign http://illinois.edu/, and the Computation Institute http://www.ci.anl.gov/. Links: http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/Events/GCC2012/Abstracts Thanks, Dave Clements -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] where can I find galaxy code documentation?
Thanks for the example, Frank.
You can upload to data libraries directly from the local filesystem. The
relevant documentation is here:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
Eli, with respect to the question about modifying galaxy-dist/lib:
Unfortunately, there's not much in the way of documentation for developing the
Galaxy application/framework itself. The code is commented to some degree. If
you have a specific question or problem you're trying to solve we can probably
point you in the right direction.
--nate
On Apr 16, 2012, at 8:54 AM, Frank Sørensen wrote:
Hi Eli,
That could easily be accomplished without changing the code, by writing a
simple tool.
The xml-file:
tool id=importer name=Import version=0.0.1 hidden=false
descriptionImport files/description
parallelism method=basic/parallelism
command interpreter=python
importer.py
-$link $infile $outfile
/command
inputs
param type=text name=infile size=180 label=Enter path to file to
upload /
param name=link type=boolean truevalue=--link checked=false
falsevalue= label=Link to file help=Should the file be linked instead of
copied into Galaxy? /
/inputs
outputs
data format=data name=outfile label=Imported file /
/outputs
help
**What it does**
This tool is a simple file importer
--
The path string points to a local file, that should be imported into the
current history.
/help
/tool
And the Python script:
#!/usr/bin/python
import argparse, os
version = '0.0.1'
progName='importer'
def __main__():
parser = argparse.ArgumentParser(
prog=progName,
description='Simple Galaxy file importer')
parser.add_argument('--version', action='version',
version='%(prog)s '+version,
help='Display version information')
parser.add_argument('infile', nargs=1,
type=str,
help='input filename mask')
parser.add_argument('savefile', nargs=1,
type=str,
help='savefile filename')
parser.add_argument('-l','--link',
action='store_true',
default=False,
help='Make symbolic link to file')
try:
args = parser.parse_args()
if args.link:
os.system('ln -fs %s %s' % (args.infile[0],args.savefile[0]))
else:
os.system('cp %s %s' % (args.infile[0],args.savefile[0]))
except Exception as E:
print sys.stderr, E
exit(1)
pass
if __name__==__main__: __main__()
I have written a handful of Galaxy tools that implements this technique, and
it works like a charm. However this specific example is copy and pasted and
simplified from one of my existing tools, so I haven't actually tried it, so
It might contain a few spelling mistooks.
With a minimum of coding, the opposite can also be implemented, namely
exporting files from galaxy to an external local file.
Kind regards
Frank Sorensen
Den 16-04-2012 08:13, Eli Reuveni skrev:
Hi,
I have a local galaxy instance in my institute and have few basic questions:
1) I need to enable galaxy to upload large files from the local galaxy
server without the need to use the ftp or the file upload module, is there
an easy way to do it or do I need to write a special code?
2) I need to customize galaxy Python code (i.e., under the
~/galaxy-dist/lib directory). Where can I find documentation of the galaxy
Python classes (using wiki or other format)
Thanks in advanced,
--
Frank Sørensen, B.Sc., Programmer
Molecular Diagnostic Laboratory (MDL)
Molekylær Medicinsk Afdeling (MOMA)
Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N
Tlf. +45 7845 5363
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Re: [galaxy-dev] This link may not be followed from within Galaxy.
On Apr 16, 2012, at 7:13 AM, Eli Reuveni wrote: Hi, I am getting the error “This link may not be followed from within Galaxy.” When I try to upload a data file to my local galaxy. I have traced back the error to root.py (RootController class). Could anyone help me with that? Hi Eli, My initial guess would be that you have enabled the nginx upload settings but that there is a misconfiguration with the upload module. If this is not the case, could you provide the URL that your browser is accessing (you should be able to find it in the Galaxy server log) to receive this error, and some details about whether you are running behind a proxy server, with a prefix, etc.? Thanks, --nate Best ___ 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] Error copying files from job_working_directory
Hello, I've integrated a tool into my Galaxy instance, but when I run the tool I get this error: galaxy.objectstore CRITICAL 2012-04-16 11:25:56,697 Error copying /home/galaxy/galaxy-dist/database/job_working_directory/000/307/dataset_431_files/unweighted_unifrac_2d_continuous to /home/galaxy/galaxy-dist/database/files/000/dataset_431_files/unweighted_unifrac_2d_continuous: [Errno 21] Is a directory: '/home/galaxy/galaxy-dist/database/job_working_directory/000/307/dataset_431_files/unweighted_unifrac_2d_continuous' As I can see, it fails because it is trying to copy a directory. Is this feature supported in Galaxy? If it is supported, what I have to do to enable copy the directories from the job_working_directory? Thank you, Jose ___ 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] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found
Hi All, I was trying to setup the Galaxy tool dependencies, and I met the following problem when running sam-to-bam in samtools: Traceback (most recent call last): File /mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 336, in finish_job drm_job_state.job_wrapper.finish( stdout, stderr ) File /mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/__init__.py, line 637, in finish dataset.set_meta( overwrite = False ) File /mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/model/__init__.py, line 875, in set_meta return self.datatype.set_meta( self, **kwd ) File /mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/datatypes/binary.py, line 179, in set_meta raise Exception, Error Setting BAM Metadata: %s % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found I already set the path of samtools Below I pasted how I set the path: ubuntu@master:/mnt/galaxyTools/tools/samtools$ ll total 8 drwxr-xr-x 4 ubuntu ubuntu 65 2012-04-16 19:09 ./ drwxr-xr-x 38 ubuntu ubuntu 4096 2012-04-16 18:41 ../ drwxr-xr-x 2 ubuntu ubuntu 53 2012-04-16 19:08 0.1.12/ drwxr-xr-x 2 ubuntu ubuntu 53 2012-04-13 20:23 0.1.7/ lrwxrwxrwx 1 ubuntu ubuntu 38 2012-04-16 19:09 default - /mnt/galaxyTools/tools/samtools/0.1.12/ ubuntu@master:/mnt/galaxyTools/tools/samtools$ more default/env.sh PATH=/mnt/galaxyTools/tools/samtools/0.1.12:$PATH I used the same way to set other programs, such as bwa and bowtie, and they worked perfectly. Only samtools could not work. I even used the full path of samtools in the wrapper file sam_to_bam.py, and it was not working neither. I am wondering if any one met the same problem, or some one can give me some hints. Thank you very much. Cai ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Workflow import error
Hi Robert, I've cc'd the galaxy-dev list on this reply since the workflow components are primarily supported by other Galaxy development team members and I'm not optimally suited to handle this issue. Please keep responses on the galaxy-dev mail list so others that are interested can follow the entire thread. You should receive a response on this soon. Thanks for sending your messages, Greg Von Kuster On Apr 16, 2012, at 5:53 PM, Robert Chase wrote: Hi Greg, When I upload my workload ga file to galaxy, I get a screen saying that some of the tools in the workflow are not available in this instance of galaxy, specifically fastqc. I downloaded fastqc into my tools directory and restarted galaxy, but when I tried to re-upload the workflow it complained again that fastqc wasn't available. Fastqc does in fact load in the tools sidebar, but when I try to run it I get the following: An error occurred running this job: Fastq failed. Error executing FastQC. /bin/sh: fastqc: command not found -Rob On Mon, Apr 16, 2012 at 10:21 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Rob, When you import a workflow into a Galaxy instance, the instance must have all tools required by the workflow available in its tool panel. I've only seen this error when the workflow requires a tool that is not available, so can you let us know if this is the case? Thanks, Greg Von Kuster On Apr 16, 2012, at 10:07 AM, Robert Chase wrote: Hi Greg, After I modified the modules.py file that bug went away, but now I'm getting a new error: Module galaxy.web.base.controller:420 in get_stored_workflow_steps view module = module_factory.from_workflow_step( trans, step ) #Check if tool was upgraded step.upgrade_messages = module.check_and_update_state() # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) step.upgrade_messages = module.check_and_update_state() AttributeError: 'NoneType' object has no attribute 'check_and_update_state' -Rob On Mon, Apr 16, 2012 at 9:19 AM, Robert Chase re...@channing.harvard.edu wrote: Thanks Greg, I'll try to merge the change into my version. -Rob On Mon, Apr 16, 2012 at 9:18 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Robert, Thanks for reporting this issue - it has been fixed in change set 7038:1fdcce63a06f, which is currently available only in our central repository. It will be available in the dist in the next update. Greg Von Kuster On Apr 13, 2012, at 5:22 PM, Robert Chase wrote: Hello All, I'm pretty sure I found a bug in the main galaxy distribution. The following code diff shows the introduction of the line tool_version = self.__get_tool_version( trans, tool_id ) but if you look at the function definition containing that line, you see def from_workflow_step( Class, trans, step ): which does not half a self in it. Then we get an error. https://bitbucket.org/galaxy/galaxy-dist/diff/lib/galaxy/workflow/modules.py?diff2=e6464387ed3fdiff1=c60760713d26 -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/ ___ 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] Error copying files from job_working_directory
Hi everybody, I was searching through the Galaxy code and I find the solution: the function responsible for copying files is using shutil.copy function, which only allows copy files. I've modified this function to use shutil.copytree in case of file_name is a directory. I can send you the code if you email me. Also, I don't know if there is a good reason against this solution. If it is, I will be very grateful if somebody can explain it. Thanks, Jose From: josenavasmol...@hotmail.com To: galaxy-dev@lists.bx.psu.edu Date: Mon, 16 Apr 2012 17:34:29 + Subject: [galaxy-dev] Error copying files from job_working_directory Hello, I've integrated a tool into my Galaxy instance, but when I run the tool I get this error: galaxy.objectstore CRITICAL 2012-04-16 11:25:56,697 Error copying /home/galaxy/galaxy-dist/database/job_working_directory/000/307/dataset_431_files/unweighted_unifrac_2d_continuous to /home/galaxy/galaxy-dist/database/files/000/dataset_431_files/unweighted_unifrac_2d_continuous: [Errno 21] Is a directory: '/home/galaxy/galaxy-dist/database/job_working_directory/000/307/dataset_431_files/unweighted_unifrac_2d_continuous' As I can see, it fails because it is trying to copy a directory. Is this feature supported in Galaxy? If it is supported, what I have to do to enable copy the directories from the job_working_directory? Thank you, Jose ___ 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] Workflow import error
Robert, It sounds like you're experiencing two separate problems to me. Let's isolating the problem to just the FastQC tool install, first, and move on from there. There is a FastQC tool in your toolbar, and execution results in the error you describe in the previous email of 'Fastq failed. Error executing FastQC. /bin/sh: fastqc command not found'. Correct? If this is the case, can you verify that you do have fastqc installed and accessible on the path of the galaxy user? And, how did you add the tool to galaxy- via toolshed or did you use the FastQC wrapper included with the primary Galaxy distribution? -Dannon On Apr 16, 2012, at 6:23 PM, Greg Von Kuster wrote: Hi Robert, I've cc'd the galaxy-dev list on this reply since the workflow components are primarily supported by other Galaxy development team members and I'm not optimally suited to handle this issue. Please keep responses on the galaxy-dev mail list so others that are interested can follow the entire thread. You should receive a response on this soon. Thanks for sending your messages, Greg Von Kuster On Apr 16, 2012, at 5:53 PM, Robert Chase wrote: Hi Greg, When I upload my workload ga file to galaxy, I get a screen saying that some of the tools in the workflow are not available in this instance of galaxy, specifically fastqc. I downloaded fastqc into my tools directory and restarted galaxy, but when I tried to re-upload the workflow it complained again that fastqc wasn't available. Fastqc does in fact load in the tools sidebar, but when I try to run it I get the following: An error occurred running this job: Fastq failed. Error executing FastQC. /bin/sh: fastqc: command not found -Rob On Mon, Apr 16, 2012 at 10:21 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Rob, When you import a workflow into a Galaxy instance, the instance must have all tools required by the workflow available in its tool panel. I've only seen this error when the workflow requires a tool that is not available, so can you let us know if this is the case? Thanks, Greg Von Kuster On Apr 16, 2012, at 10:07 AM, Robert Chase wrote: Hi Greg, After I modified the modules.py file that bug went away, but now I'm getting a new error: Module galaxy.web.base.controller:420 in get_stored_workflow_steps view module = module_factory.from_workflow_step( trans, step ) #Check if tool was upgraded step.upgrade_messages = module.check_and_update_state() # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) step.upgrade_messages = module.check_and_update_state() AttributeError: 'NoneType' object has no attribute 'check_and_update_state' -Rob On Mon, Apr 16, 2012 at 9:19 AM, Robert Chase re...@channing.harvard.edu wrote: Thanks Greg, I'll try to merge the change into my version. -Rob On Mon, Apr 16, 2012 at 9:18 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Robert, Thanks for reporting this issue - it has been fixed in change set 7038:1fdcce63a06f, which is currently available only in our central repository. It will be available in the dist in the next update. Greg Von Kuster On Apr 13, 2012, at 5:22 PM, Robert Chase wrote: Hello All, I'm pretty sure I found a bug in the main galaxy distribution. The following code diff shows the introduction of the line tool_version = self.__get_tool_version( trans, tool_id ) but if you look at the function definition containing that line, you see def from_workflow_step( Class, trans, step ): which does not half a self in it. Then we get an error. https://bitbucket.org/galaxy/galaxy-dist/diff/lib/galaxy/workflow/modules.py?diff2=e6464387ed3fdiff1=c60760713d26 -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/ ___ 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/
