Re: [galaxy-dev] Workflow Queue
Hi Edward Select 'view' instead of 'run' in your workflow list. This will give you a nice (human readable) overview of all the steps, or select the download option to get an xml describing your workflow. Regards, Hans On 09/13/2012 03:20 AM, Edward Hills wrote: Hi Galaxy team, I am wanting to know where to find the queue that stores all tool's that are going to be executed in the pipeline. For example, I am running a workflow of 5 tools all linked together (the details are not important). Programatically I wish to know the names of the tools that are going to be run. This is because I wish to perform some pre-run analysis on all the tools in the workflow before they get executed. Thanks, Edward Hills Department of Biochemistry, University of Otago, Dunedin, New Zealand. ___ 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] Workflow Queue
Hi Galaxy team, I am wanting to know where to find the queue that stores all tool's that are going to be executed in the pipeline. For example, I am running a workflow of 5 tools all linked together (the details are not important). Programatically I wish to know the names of the tools that are going to be run. This is because I wish to perform some pre-run analysis on all the tools in the workflow before they get executed. Thanks, Edward Hills Department of Biochemistry, University of Otago, Dunedin, New Zealand. ___ 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] Size of the genome indexes repos in Galaxy Main
Hi guys, Just a quick question about the total size of the genome indexes just made available via rsync server? Cheers, Derrick ___ 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] Automatic installation of third party dependancies
Hi Lance,
What is the changeset revision that you installed? It looks like you could
only have installed one of the following 3 revisions:
1:14e18dc9ed13
2:f5d08224af89
4:14bec14f4290
Since you could not have installed 3:f7a5b54a8d4f, I'm not quite sure how you
could be trying to update to 4. Did you install 4 and are trying to get
updates?
I've tried several things but am not able to reproduce this behavior, so it's
difficult to determine what may be causing the problem
Greg Von Kuster
On Sep 12, 2012, at 3:08 PM, Lance Parsons wrote:
> I've updated my development system now, and when I try to get updates for
> that particular tool (htseq_count) I run into the following error. Any ideas
> on how I can/should fix this? Thanks.
>
> URL:
> http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/&name=htseq_count&owner=lparsons&changeset_revision=f7a5b54a8d4f&latest_changeset_revision=14bec14f4290&latest_ctx_rev=4
> File
> '/data/galaxy-dev/galaxy-dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
> line 364 in respond
> app_iter = self.application(environ, detect_start_response)
> File
> '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
> line 98 in __call__
> environ, self.app)
> File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
> line 539 in intercept_output
> app_iter = application(environ, replacement_start_response)
> File
> '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
> line 80 in __call__
> return self.application(environ, start_response)
> File
> '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/middleware/remoteuser.py',
> line 91 in __call__
> return self.app( environ, start_response )
> File
> '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
> line 632 in __call__
> return self.application(environ, start_response)
> File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/base.py', line 160
> in __call__
> body = method( trans, **kwargs )
> File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/__init__.py', line
> 184 in decorator
> return func( self, trans, *args, **kwargs )
> File
> '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/controllers/admin_toolshed.py',
> line 1469 in update_to_changeset_revision
> update_repository( repo, latest_ctx_rev )
> File '/data/galaxy-dev/galaxy-dev/lib/galaxy/util/shed_util.py', line 1655 in
> update_repository
> rev=ctx_rev )
> File
> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/commands.py',
> line 5661 in update
> rev = scmutil.revsingle(repo, rev, rev).rev()
> File
> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py',
> line 515 in revsingle
> l = revrange(repo, [revspec])
> File
> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py',
> line 588 in revrange
> for r in m(repo, range(len(repo))):
> File
> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
> line 1414 in mfunc
> return getset(repo, subset, tree)
> File
> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
> line 156 in getset
> return methods[x[0]](repo, subset, *x[1:])
> File
> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
> line 171 in symbolset
> return stringset(repo, subset, x)
> File
> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
> line 161 in stringset
> x = repo[x].rev()
> File
> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/localrepo.py',
> line 235 in __getitem__
> return context.changectx(self, changeid)
> File
> '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/context.py',
> line 103 in __init__
> _("unknown revision '%s'") % changeid)
> RepoLookupError: unknown revision '4'
>
>
> Lance Parsons wrote:
>>
>> Thanks Greg. I used you're updated version and added numpy as a
>> separate dependency. It seems to work in my development system. I
>> haven't updated my qa or production versions yet, so I can't check
>> there. Perhaps you could test it and let me know if there are issues, etc.
>>
>> Glad I can be of help.
>>
>> Lance
>>
>> Greg Von Kuster wrote:
>>>
>>> Hello Lance,
>>>
>>> See my inline comments.
>>>
>>>
>>> On Sep 4, 2012, at 3:15 PM, Lance Parsons wrote:
>>>
I've put together a tool wrapper for the htseq-count script that is part
of the HTSeq python package and uploaded that to the tool shed. However,
I have discovered that the tool dependancies do not install properly.
There are a couple of issues that I've run into.
1) The biggest issue is
Re: [galaxy-dev] environment variables and paths for toolshed tools
Hi David,
With the exception of requiring versions strings in tags in the
tool config in order to enable versioned tool dependency installation (which is
documented in the tool shed wiki at
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories),
this is the first change to the way Galaxy tool configs should be written.
I'll get a wiki put together for this new enhancement as soon as possible. I'm
hoping to have it as part of the next Galaxy dist release when the feature is
released.
Greg Von Kuster
On Sep 12, 2012, at 1:47 PM, David Hoover wrote:
> On the topic of toolshed tools, is there any documented guidance about how to
> create a tool for the toolshed? There is some syntactical help on the wiki,
> but no comprehensive guide.
>
> On Sep 12, 2012, at 1:41 PM, Greg Von Kuster wrote:
>
>> It'll be available in Galaxy central sooner than Galaxy dist. I'll send you
>> an email when I commit it.
>>
>> On Sep 12, 2012, at 1:31 PM, David Hoover wrote:
>>
>>> Will it be available through galaxy-dist or galaxy-central? I have started
>>> using the galaxy-central repository just to be on the bleeding edge.
>>>
>>> On Sep 12, 2012, at 1:15 PM, Greg Von Kuster wrote:
>>>
Hello David,
This is not currently possible, but will be available in the next Galaxy
distribution release, currently scheduled for about 10 days from now. You
will include a tool_dependencies.xml file in your tool shed repository
that looks something like the following.
>>> action="set_to">$INSTALL_DIR
Your tool will find the required files via the defined JAVA_JAR_PATH by
using a tag set in the tool config, something like this:
JAVA_JAR_PATH
The tag in the tool config would be something like this:
python_wrapper.py $JAVA_JAR_PATH/some_file.jar $param1 $param2...
I'm close to having this working, so if you are interested in testing
before the next Galaxy dist release, let me know and I'll tell you when
the Galaxy central repository has the new feature.
Thanks!
Greg Von Kuster
On Sep 12, 2012, at 1:00 PM, David Hoover wrote:
> Are there any environment variables that are honored by toolshed
> installed tools? I tried creating a tool that uses
> ${GALAXY_DATA_INDEX_DIR} or $GALAXY_HOME, then uploaded it the test
> toolshed, then installed it automatically. Neither of these resolved to
> what I expected. I don't want to hard-code the path in the xml tool
> file, but rather have a default location for other executables and jar
> files. How should this best be done?
>
> David Hoover
> Helix Systems Staff
> ___
> 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"
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and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] toolshed upload problem
Hi David, Can you send me your tarball? Thanks, Greg Von Kuster On Sep 12, 2012, at 6:16 PM, David Hoover wrote: > I've created a repository in the test toolshed and tried uploading gzipped > tarballs with all files required. I have several tool config files (.xml) > wrapping a single python script with some tool-data dependencies. > > If I upload a single tool config file with the dependencies, everything is > ok. However, if I try uploading more than one config file at a time, it > complains with the error message for all but one of the config files: > > *.xml - This file requires an entry for "'gatk2_picard_indexes'" in the > tool_data_table_conf.xml file. Upload a file named > tool_data_table_conf.xml.sample to the repository that includes the required > entry to correct this error. > > The tool_data_table_conf.xml.sample file already exists within the tarball. > Nothing changes if I upload the file separately. > > Any ideas? > > David Hoover > Helix Systems Staff > ___ > 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] toolshed upload problem
I've created a repository in the test toolshed and tried uploading gzipped tarballs with all files required. I have several tool config files (.xml) wrapping a single python script with some tool-data dependencies. If I upload a single tool config file with the dependencies, everything is ok. However, if I try uploading more than one config file at a time, it complains with the error message for all but one of the config files: *.xml - This file requires an entry for "'gatk2_picard_indexes'" in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct this error. The tool_data_table_conf.xml.sample file already exists within the tarball. Nothing changes if I upload the file separately. Any ideas? David Hoover Helix Systems Staff ___ 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] FreeBayes Installation Bug
Hi Lance, Thank you for finding this issue and a bigger thanks for the patch. We've updated FreeBayes in the toolshed with your patch. Please let us know if you encounter further issues. Thanks! Dan On Sep 11, 2012, at 5:08 PM, Lance Parsons wrote: > Today I ran into a new issues with installing a specific version of > Freebayes. It turns out to be an issue with how git deals with submodules, > something I'm only just learning about myself. In order to ensure that > FreeBayes is built with the correct versions of all of the various submodules > for the desired revision, it seems that two commands are needed: > > git checkout 9608597d12e127c847ae03aa03440ab63992fedf > git submodule update --recursive > > In the current version of tool_dependencies.xml, there is a git reset --hard > 9608597d12e127c847ae03aa03440ab63992fedf which seems to work similarly to the > checkout command above, however, it does not put the submodules back at the > correct revisions. That is only now an issue since they were updated only > recently. > > I've attached a patch to the tool_dependencies.xml file that should once > again allow FreeBayes to be built and installed automatically. It would be > great if you could update the Tool Shed repo. Thanks. > > -- > 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/
Re: [galaxy-dev] Redirect log files?
On Sep 12, 2012, at 1:09 PM, Fields, Christopher J wrote: > Simple question: is there a way within universe_wsgi.ini to point to a > specific location where Galaxy log (and possibly PID) files can be dropped? > I've searched for this but couldn't find an answer beyond locally modifying > run.sh, but it's entirely possible I'm missing something obvious. > > We want to have the logs stored on the server side in /var/log or /var/spool, > not on our NFS share. The way run.sh is currently grabbing server > information it seems as if we need to have something like this in the > [server:*] config section: > > [server:/var/log/galaxy/web0] > > which doesn't seem right. Maybe something like the following (per server)? > > [server:web0] > use = egg:Paste#http > port = 8080 > host = 127.0.0.1 > use_threadpool = true > threadpool_workers = 7 > log_dir=/var/log/galaxy/ > > or simply (for all log and/or PID files): > > log_dir=/var/log/galaxy/ Hi Chris, It can't be done through the config file. You have to use the --log-file and --pid-file from the command line. --nate > > chris > ___ > 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] cufflinks and cuffdiff FPKM values
Hello everyone, I am comparing two samples (control and treated) paired end RNA Seq data. I am getting different FPKM values on my cufflinks output of 2 samples when compared to the 2 values that cuffdiff.. Below is the snap shot of a gene with different FPKM values. (I am not displaying the gene name). Cufflinks output: Gene length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status Sample xyz - - 39.9094 38.9553 40.8635 OK Control xyz - - 19.4664 18.7786 20.1542 OK Treated cuffdiff output: Gene sample_1 sample_2 status value_1/Control value_2/ treated log2(fold_change) test_stat p_value q_value significant xyz q1 q2 OK 59.6706 27.1551 -1.1358 5.06151 4.16E-07 4.00E-05 yes I am assuming that FPKM values from cufflinks and cuffdiff output should be matching. Any kind of suggestions are appreciated. 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/
Re: [galaxy-dev] Automatic installation of third party dependancies
I've updated my development system now, and when I try to get updates
for that particular tool (htseq_count) I run into the following error.
Any ideas on how I can/should fix this? Thanks.
URL:
http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/&name=htseq_count&owner=lparsons&changeset_revision=f7a5b54a8d4f&latest_changeset_revision=14bec14f4290&latest_ctx_rev=4
File
'/data/galaxy-dev/galaxy-dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File
'/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File
'/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File
'/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/middleware/remoteuser.py',
line 91 in __call__
return self.app( environ, start_response )
File
'/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/base.py',
line 160 in __call__
body = method( trans, **kwargs )
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/__init__.py',
line 184 in decorator
return func( self, trans, *args, **kwargs )
File
'/data/galaxy-dev/galaxy-dev/lib/galaxy/web/controllers/admin_toolshed.py',
line 1469 in update_to_changeset_revision
update_repository( repo, latest_ctx_rev )
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/util/shed_util.py', line
1655 in update_repository
rev=ctx_rev )
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/commands.py',
line 5661 in update
rev = scmutil.revsingle(repo, rev, rev).rev()
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py',
line 515 in revsingle
l = revrange(repo, [revspec])
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py',
line 588 in revrange
for r in m(repo, range(len(repo))):
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
line 1414 in mfunc
return getset(repo, subset, tree)
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
line 156 in getset
return methods[x[0]](repo, subset, *x[1:])
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
line 171 in symbolset
return stringset(repo, subset, x)
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
line 161 in stringset
x = repo[x].rev()
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/localrepo.py',
line 235 in __getitem__
return context.changectx(self, changeid)
File
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/context.py',
line 103 in __init__
_("unknown revision '%s'") % changeid)
RepoLookupError: unknown revision '4'
Lance Parsons wrote:
Thanks Greg. I used you're updated version and added numpy as a
separate dependency. It seems to work in my development system. I
haven't updated my qa or production versions yet, so I can't check
there. Perhaps you could test it and let me know if there are issues, etc.
Glad I can be of help.
Lance
Greg Von Kuster wrote:
Hello Lance,
See my inline comments.
On Sep 4, 2012, at 3:15 PM, Lance Parsons wrote:
I've put together a tool wrapper for the htseq-count script that is
part of the HTSeq python package and uploaded that to the tool
shed. However, I have discovered that the tool dependancies do not
install properly. There are a couple of issues that I've run into.
1) The biggest issue is the inability to set both the PYTHONPATH and
PATH environment variables as part of installation. If I put two
separate tags, then the second
overwrites the first in the env.sh file. If instead, I put
two tags within the action, only one (the
second) gets executed during installation.
The above issues have been corrected in changeset 7621:108cda898646,
which is currently available only in the Galaxy central repository.
There is a new Galaxy distribution scheduled to go out today, but
unfortunately this changeset will not be included. From here on,
Galaxy releases are tentatively scheduled for every 2 weeks, so if
you don't want to pull from the Galaxy central repository, the fix
should be available in the next release 2 weeks from now.
I've slightly altered your tool_
Re: [galaxy-dev] environment variables and paths for toolshed tools
Hello David,
This is not currently possible, but will be available in the next Galaxy
distribution release, currently scheduled for about 10 days from now. You will
include a tool_dependencies.xml file in your tool shed repository that looks
something like the following.
$INSTALL_DIR
Your tool will find the required files via the defined JAVA_JAR_PATH by using a
tag set in the tool config, something like this:
JAVA_JAR_PATH
The tag in the tool config would be something like this:
python_wrapper.py $JAVA_JAR_PATH/some_file.jar $param1 $param2...
I'm close to having this working, so if you are interested in testing before
the next Galaxy dist release, let me know and I'll tell you when the Galaxy
central repository has the new feature.
Thanks!
Greg Von Kuster
On Sep 12, 2012, at 1:00 PM, David Hoover wrote:
> Are there any environment variables that are honored by toolshed installed
> tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or
> $GALAXY_HOME, then uploaded it the test toolshed, then installed it
> automatically. Neither of these resolved to what I expected. I don't want
> to hard-code the path in the xml tool file, but rather have a default
> location for other executables and jar files. How should this best be done?
>
> David Hoover
> Helix Systems Staff
> ___
> 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] Redirect log files?
Simple question: is there a way within universe_wsgi.ini to point to a specific location where Galaxy log (and possibly PID) files can be dropped? I've searched for this but couldn't find an answer beyond locally modifying run.sh, but it's entirely possible I'm missing something obvious. We want to have the logs stored on the server side in /var/log or /var/spool, not on our NFS share. The way run.sh is currently grabbing server information it seems as if we need to have something like this in the [server:*] config section: [server:/var/log/galaxy/web0] which doesn't seem right. Maybe something like the following (per server)? [server:web0] use = egg:Paste#http port = 8080 host = 127.0.0.1 use_threadpool = true threadpool_workers = 7 log_dir=/var/log/galaxy/ or simply (for all log and/or PID files): log_dir=/var/log/galaxy/ chris ___ 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] environment variables and paths for toolshed tools
Are there any environment variables that are honored by toolshed installed
tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or
$GALAXY_HOME, then uploaded it the test toolshed, then installed it
automatically. Neither of these resolved to what I expected. I don't want to
hard-code the path in the xml tool file, but rather have a default location for
other executables and jar files. How should this best be done?
David Hoover
Helix Systems Staff
___
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:
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Re: [galaxy-dev] Recovery of broken toolshed installs
Hi Alex, Assuming the installed repository is stuck in a "Cloning" state (you can see this by clicking the Admin menu link "Manage installed tool shed repositories"), you can fix it by manually running the following sql command in your db environment (string case is required). update tool_shed_repository set status = 'New' where status = 'Cloning'; If the status is not 'Cloning', you may need to remove the directory where the repository was in the process of being cloned as well, and perhaps manually delete the any tool entries from you shed_tool_conf.xml file. This process is currently manual, but the next release of Galaxy (coming in about 10 days) will provide the ability to do this via a Galaxy Admin UI feature. Greg Von Kuster On Sep 11, 2012, at 11:48 PM, Oleksandr Moskalenko wrote: > Hi Greg, > > What's the best way to completely clean up a borked repository on disk and in > the Galaxy database that failed to install for any odd reason, but hangs > around causing Apache server errors [1] on any action afterwards? > > Thanks, > > Alex > > 1. "Server Error. An error occurred. See the error logs for more information. > (Turn debug on to display exception reports here)" ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy error
On Wed, Sep 12, 2012 at 12:16 AM, Kenneth R. Auerbach wrote: > Hello, > > Can anyone tell me why I keep getting this error when I try to do a blast > search in Galaxy? I checked that the nr database file was there and had the > right permissions. Does this error mean that Galaxy can't find the nr file > or does it mean something else? > > > An error occurred running this job:BLAST Database error: No alias or index > file found for protein database > [/9720/genome_references/ncbi/nr-protein-db/nr-newstyle/nr] in search path > [/9720/galaxyprod/galaxy-dist/database/job_working_directory/1485::] > Return error code 2 from command: > blast > - > > Thank you. > Ken. I already replied to this question when you asked yesterday (and used a more specific email subject - "Galaxy error" is not helpful): http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-September/011066.html Regards, 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/
