Re: [galaxy-dev] visualization button
Hi Philip The appearance of the visualization button depends on the datatype of your output. E.g. when it is set to 'tabular', you should get the button allowing you to create a scatter plot. However, depending on your data, it might not make much sense to visualize it in 'Trackster', 'Circster' or as scatter plot. Regards, Hans-Rudolf On 04/07/2014 02:11 AM, Philippe Moncuquet wrote: Hi, I have developed a simple script that give some statistics on an assemble. It generates a tabular output. The visualization button is not available when I extend the output in the history pane. Is there any code that I need to put in my xml wrapper to get this button available ? Regards, Philip ___ 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] Access a tool inside another tool
Hi, For testing I have installed custom tool A and its repository dependency custom tool B. Actually as per the implementation there is no dependency among these two custom tools. But in general if we want to access a tool inside another tool implementation how should I do that. Can you please share resources with me if any. Thanks, JanakiRam ___ 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] The PBS job did not stop after the running dataset was deleted
Hi, I used the torque/pbs system with Galaxy In the newer stable version (2014.2.10), the PBS job did not stop when I deleted the running dataset. It can be deleted with such API: http://127.0.0.1:8080/datasets/f2db41e1fa331b3e/delete_async Seems the js did not work? Regards, Jian-Long ___ 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] Fwd: [galaxy-user] known name outputs shown in /database/files but not in galaxy windows
Hi Jen,
I tried what you explain, but still doens't work.
I did create a new datatype, gem. And I modified my code as you suggested.
The tool i'm using always generates by default two archives . gem and .log.
Those are the ones that I can't show in the galaxy interface, the output I
get is empty, the dataset_54.dat and the dataset_55.dat. I can't handle to
show me the .dat.gem and .dat.log ones.
dataset_54.dat (my first declared output that it's empty)
dataset_54.dat.gem (the output that throws the tool)
dataset_54.dat.log (the other output file that throws the tool)
dataset_55.dat (my second declared output that it's empty)
Here it is the gem_indexer.xml
tool id=GEM Index name=create GEM Indexer
command interpreter=python gem_indexer.py $input $output1
$output2/command
inputs
param name=input type=data format=fasta label=Fichero de
entrada(formato .fas) /
/inputs
stdio
exit_code range=1: level=fatal description=Bad input dataset
/
/stdio
outputs
data format_source=gem name=output1 label=${tool.name} on
${on_string}: salida from_work_dir=gem_tools/salida.gem /
data format_source=tab name=output2 label=${tool.name} on
${on_string}: salida from_work_dir=gem_tools/salida.log /
/outputs
/tool
And the gem_indexer.py
import sys,os
def __main__():
# Command to run GEM tool. Here the Gem indexer is getting invoked along
with arguments to be passed.
cmd=gem-indexer -i +sys.argv[1]+ -o salida
os.system(cmd)
if __name__ == __main__ : __main__()
2014-04-04 6:05 GMT+02:00 Jennifer Jackson j...@bx.psu.edu:
Reply posted:
http://dev.list.galaxyproject.org/known-name-outputs-shown-in-database-files-but-not-in-galaxy-windows-tt4664079.html
Angelica,
Next time it would be great to post to only a single list. The
galaxy-...@bx.psu.edu list is best for this type of question.
Take care,
Jen
Galaxy team
On 4/3/14 12:13 AM, ANGELICA GOMEZ ROIG wrote:
I have made a wrapper that has a tool that giving it an input file,
gives you two output files with known extension: .gem and .log
I call the tool with a python file, and I pass it the input file and the
two output file names for galaxy to show them, but when I look into de
database/files/000/ i get four files:
dataset_54.dat (my first declared output that it's empty)
dataset_54.dat.gem (the output that throws the tool)
dataset_54.dat.log (the other output file that throws the tool)
dataset_55.dat (my second declared output that it's empty)
So,what I'm getting in the galaxy interface is _54.dat and _55.dat, both
empty, instead of _54.dat.gem and _54.dat.log that are the good ones. How
can I fix these?
Thanks
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Re: [galaxy-dev] Stopping Upload jobs
Hello Carrie, I put an artificial sleep into upload.py and tried to replicate this with the local, DRMAA, and SLURM job runners but could not. I was working out of galaxy-central instead of galaxy-dist s it is possible it has been fixed since the last dist update - the history panel has seen a lot of development. Can you let us know if the problem persists after the next upgrade (I think it will be out in a couple weeks)? -John On Thu, Apr 3, 2014 at 2:15 PM, Ganote, Carrie L cgan...@iu.edu wrote: Hi List, I've noticed that the mechanisms for catching job termination signals don't seem to apply to uploading jobs. I was having trouble with *any* jobs being terminated until I pulled Nate's changeset 1298d3f from Galaxy central, but it still doesn't work for uploads. It will remove them from the history, but if I restart Galaxy, they are put back into the history (whether or not there is anything actually happening). If the upload.py script is actively running and I delete the job, the history item comes back up during the next watch cycle. I've been experimenting with staging files as part of a job and I notice that if I set the job state to upload during the staging, the job never gets marked as deleted or deleted_new if I try to remove it from the history with the X button - so the logic I have to stop the upload is never run. Thanks for any insight, Carrie Ganote ___ 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] Fwd: [galaxy-user] known name outputs shown in /database/files but not in galaxy windows
On Sat, Apr 5, 2014 at 8:07 AM, ANGELICA GOMEZ ROIG
nirvanargr2...@gmail.com wrote:
Hi Jen,
I tried what you explain, but still doens't work.
I did create a new datatype, gem. And I modified my code as you suggested.
The tool i'm using always generates by default two archives . gem and .log.
Those are the ones that I can't show in the galaxy interface, the output I
get is empty, the dataset_54.dat and the dataset_55.dat. I can't handle to
show me the .dat.gem and .dat.log ones.
dataset_54.dat (my first declared output that it's empty)
dataset_54.dat.gem (the output that throws the tool)
dataset_54.dat.log (the other output file that throws the tool)
dataset_55.dat (my second declared output that it's empty)
Here it is the gem_indexer.xml
tool id=GEM Index name=create GEM Indexer
command interpreter=python gem_indexer.py $input $output1
$output2/command
inputs
param name=input type=data format=fasta label=Fichero de
entrada(formato .fas) /
/inputs
stdio
exit_code range=1: level=fatal description=Bad input dataset
/
/stdio
outputs
data format_source=gem name=output1 label=${tool.name} on
${on_string}: salida from_work_dir=gem_tools/salida.gem /
data format_source=tab name=output2 label=${tool.name} on
${on_string}: salida from_work_dir=gem_tools/salida.log /
/outputs
/tool
And the gem_indexer.py
import sys,os
def __main__():
# Command to run GEM tool. Here the Gem indexer is getting invoked along
with arguments to be passed.
cmd=gem-indexer -i +sys.argv[1]+ -o salida
os.system(cmd)
if __name__ == __main__ : __main__()
Since you are using a wrapper script already, I would add
lines to rename the generated files (based on sys.argv[1]
plus the extensions) to the filename Galaxy is providing
(here sys.argv[2] and sys.argv[3]).
Peter
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Re: [galaxy-dev] Fwd: [galaxy-user] known name outputs shown in /database/files but not in galaxy windows
Just to add to what Peter said - you definitely don't want to use
from_work_dir and reference the outputs ($output1) in the same
command. If you know where the file is going to be relative to your
working directory there should be no reason to pass it to your script.
Also I think you want format instead of format_source as the attribute
on output.
On Mon, Apr 7, 2014 at 8:49 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Sat, Apr 5, 2014 at 8:07 AM, ANGELICA GOMEZ ROIG
nirvanargr2...@gmail.com wrote:
Hi Jen,
I tried what you explain, but still doens't work.
I did create a new datatype, gem. And I modified my code as you suggested.
The tool i'm using always generates by default two archives . gem and .log.
Those are the ones that I can't show in the galaxy interface, the output I
get is empty, the dataset_54.dat and the dataset_55.dat. I can't handle to
show me the .dat.gem and .dat.log ones.
dataset_54.dat (my first declared output that it's empty)
dataset_54.dat.gem (the output that throws the tool)
dataset_54.dat.log (the other output file that throws the tool)
dataset_55.dat (my second declared output that it's empty)
Here it is the gem_indexer.xml
tool id=GEM Index name=create GEM Indexer
command interpreter=python gem_indexer.py $input $output1
$output2/command
inputs
param name=input type=data format=fasta label=Fichero de
entrada(formato .fas) /
/inputs
stdio
exit_code range=1: level=fatal description=Bad input dataset
/
/stdio
outputs
data format_source=gem name=output1 label=${tool.name} on
${on_string}: salida from_work_dir=gem_tools/salida.gem /
data format_source=tab name=output2 label=${tool.name} on
${on_string}: salida from_work_dir=gem_tools/salida.log /
/outputs
/tool
And the gem_indexer.py
import sys,os
def __main__():
# Command to run GEM tool. Here the Gem indexer is getting invoked along
with arguments to be passed.
cmd=gem-indexer -i +sys.argv[1]+ -o salida
os.system(cmd)
if __name__ == __main__ : __main__()
Since you are using a wrapper script already, I would add
lines to rename the generated files (based on sys.argv[1]
plus the extensions) to the filename Galaxy is providing
(here sys.argv[2] and sys.argv[3]).
Peter
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Re: [galaxy-dev] The PBS job did not stop after the running dataset was deleted
Yes, there was a bug in the latest release that was fixed by Nate after the release. Full details are available in this thread: http://dev.list.galaxyproject.org/Persistent-jobs-in-cluster-queue-even-after-canceling-job-in-galaxy-tt4663719.html -John On Sun, Apr 6, 2014 at 2:24 AM, Jian-Long Huang jianl...@ntu.edu.tw wrote: Hi, I used the torque/pbs system with Galaxy In the newer stable version (2014.2.10), the PBS job did not stop when I deleted the running dataset. It can be deleted with such API: http://127.0.0.1:8080/datasets/f2db41e1fa331b3e/delete_async Seems the js did not work? Regards, Jian-Long ___ 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] authorize non admin user to only link a directory of files
Hi, we recently activated the feature for non admin users which allows them to upload a directory of files: ... # Add an option to the library upload form which allows authorized # non-administrators to upload a directory of files. The configured directory # must contain sub-directories named the same as the non-admin user's Galaxy # login ( email ). The non-admin user is restricted to uploading files or # sub-directories of files contained in their directory. #user_library_import_dir = None user_library_import_dir = /opt/galaxy/galaxy-share/ ... However we would like to restrict the permission to only link to their files without copying them into galaxy, is this possible? Greetings, Thomas --- Thomas Berner Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants - Erwin Baur-Straße 27 06484 Quedlinburg - Germany - Phone: ++49 ( 0 ) 3946 47 562 EMail: thomas.ber...@jki.bund.de ___ 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] authorize non admin user to only link a directory of files
I think you need to hack up the Galaxy code to accomplish this. There is information on how to start doing this in the following thread I think: http://dev.list.galaxyproject.org/FTP-Problem-Users-cannot-see-their-uploads-files-tp4619709p4662701.html This may just work for admin users though, I don't recall. It is hopefully a helpful start though. -John On Mon, Apr 7, 2014 at 9:02 AM, Berner, Thomas thomas.ber...@jki.bund.de wrote: Hi, we recently activated the feature for non admin users which allows them to upload a directory of files: ... # Add an option to the library upload form which allows authorized # non-administrators to upload a directory of files. The configured directory # must contain sub-directories named the same as the non-admin user's Galaxy # login ( email ). The non-admin user is restricted to uploading files or # sub-directories of files contained in their directory. #user_library_import_dir = None user_library_import_dir = /opt/galaxy/galaxy-share/ ... However we would like to restrict the permission to only link to their files without copying them into galaxy, is this possible? Greetings, Thomas --- Thomas Berner Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants - Erwin Baur-Straße 27 06484 Quedlinburg - Germany - Phone: ++49 ( 0 ) 3946 47 562 EMail: thomas.ber...@jki.bund.de ___ 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] Data manager for the BLAST database *.loc files?
Hi Daniel, Would you be OK with me/us incorporating your example Galaxy Data Manager [1] for NCBI BLAST databases http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_blastdb_ncbi_update_blastdb into the Galaxy BLAST wrappers repository https://github.com/peterjc/galaxy_blast/ under the MIT licence, and then extending it? If you have a GitHub account I can do that as a commit with you as the author to make the attribution explicit. See also https://github.com/peterjc/galaxy_blast/issues/22 where we're discussing this issue. Thanks, Peter [1] This is described in Daniel's new paper, Blankenberg et al (2014) Wrangling Galaxy's reference data http://dx.doi.org/10.1093/bioinformatics/btu119 and the Galaxy wiki: https://wiki.galaxyproject.org/Admin/Tools/DataManagers ___ 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] [CONTENT] Re: Re: Re: Re: Re: Unable to remove old datasets
Hi Nate, I have waited for all 3 instances of dataset 301 in history_dataset_association to be older than 30 days. Then I re-ran the admin script. As expected all 3 instances now have TRUE as there deleted status. I then tried the following commands as you suggested: python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 30 -6 -r $@ python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 30 -3 -r $@ I set -d to 30 and not 0; I didn't want to risk deleting other datasets. However, there was no effect. The two executions' STDOUT stated 0 datasets affected, and dataset 301 is still on disk. Will the process only work if –d is set to 0? I didn't think it would make a difference since all instances of dataset 301 are older than 30 days. -- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 -- From: Nate Coraor n...@bx.psu.edumailto:n...@bx.psu.edu Date: Friday, April 4, 2014 2:37 PM To: Ravi Sanka rsa...@jcvi.orgmailto:rsa...@jcvi.org Cc: Carl Eberhard carlfeberh...@gmail.commailto:carlfeberh...@gmail.com, Peter Cock p.j.a.c...@googlemail.commailto:p.j.a.c...@googlemail.com, galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: [CONTENT] Re: Re: Re: [galaxy-dev] Re: Re: Unable to remove old datasets Hi Ravi, I believe admin_cleanup_datasets.py only works on database times. The rest of your assumptions are likely correct, although without looking at more details of the database I can't confirm. --nate On Fri, Mar 28, 2014 at 5:12 PM, Sanka, Ravi rsa...@jcvi.orgmailto:rsa...@jcvi.org wrote: Hi Nate, I checked and there are 3 rows of dataset 301 in the history_dataset_association table (none in library_dataset_dataset_association): dataset_id create_time update_time deleted 301 2/14/14 18:49 3/25/14 20:27 TRUE 301 3/6/14 15:483/25/14 18:41 TRUE 301 3/6/14 20:113/6/14 20:11FALSE The one with the most recent create_time has its deleted status set to false. The other 2, older ones are true. I would have guessed that the most recent create_time instance is still false due being created within 30 days, but the second most recent is only 5 hours older and is set to true. Perhaps that instance was deleted by its user. That would cause its deleted status to become true, correct? I assume that if I were to wait until all 3 instances' create_times are past 30 days, my process will work, as admin_cleanup_datasets.py will set all 3 instances to false. Perchance, is there any setting on admin_cleanup_datasets.py that would cause it to judge datasets by their physical file's timestamp instead? -- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743tel:301-795-7743 -- From: Nate Coraor n...@bx.psu.edumailto:n...@bx.psu.edu Date: Friday, March 28, 2014 1:56 PM To: Ravi Sanka rsa...@jcvi.orgmailto:rsa...@jcvi.org Cc: Carl Eberhard carlfeberh...@gmail.commailto:carlfeberh...@gmail.com, Peter Cock p.j.a.c...@googlemail.commailto:p.j.a.c...@googlemail.com, galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: [CONTENT] Re: Re: [galaxy-dev] Re: Re: Unable to remove old datasets Hi Ravi, Can you check whether any other history_dataset_association or library_dataset_dataset_association rows exist which reference the dataset_id that you are attempting to remove? When you run admin_cleanup_datasets.py, it'll set history_dataset_association.deleted = true. After that is done, you need to run cleanup_datasets.py with the `-6 -d 0` option to mark dataset.deleted = true, followed by `-3 -d 0 -r ` to remove the dataset file from disk and set dataset.purged = true. Note that the latter two operations will not do anything until *all* associated history_dataset_association and library_dataset_dataset_association rows are set to deleted = true. --nate On Fri, Mar 28, 2014 at 1:52 PM, Sanka, Ravi rsa...@jcvi.orgmailto:rsa...@jcvi.org wrote: Hi Nate, I checked the dataset's entry in history_dataset_association, and the value in field deleted is true. But if this does not enable the cleanup scripts to remove the dataset from disk, then how can I accomplish that? As an admin, my intention is to completely remove datasets that are past a certain age from Galaxy, including all instances of the dataset that may exist, regardless of whether or not the various users who own said instances have deleted them from their histories. Can this be done with admin_cleanup_datasets.py? If so, how? -- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute
Re: [galaxy-dev] Data manager for the BLAST database *.loc files?
Hi Peter, It would be great to have the BLAST tools use tool data tables and Data Managers. Let me know what I can do to help. Thanks, Dan On Apr 7, 2014, at 11:48 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Daniel, Would you be OK with me/us incorporating your example Galaxy Data Manager [1] for NCBI BLAST databases http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_blastdb_ncbi_update_blastdb into the Galaxy BLAST wrappers repository https://github.com/peterjc/galaxy_blast/ under the MIT licence, and then extending it? If you have a GitHub account I can do that as a commit with you as the author to make the attribution explicit. See also https://github.com/peterjc/galaxy_blast/issues/22 where we're discussing this issue. Thanks, Peter [1] This is described in Daniel's new paper, Blankenberg et al (2014) Wrangling Galaxy's reference data http://dx.doi.org/10.1093/bioinformatics/btu119 and the Galaxy wiki: https://wiki.galaxyproject.org/Admin/Tools/DataManagers ___ 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] Data manager for the BLAST database *.loc files?
On Mon, Apr 7, 2014 at 5:38 PM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Peter, It would be great to have the BLAST tools use tool data tables and Data Managers. Let me know what I can do to help. Thanks, Dan That's great Dan - I see you've commented on GitHub, so we can continue this there: https://github.com/peterjc/galaxy_blast/issues/22 Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] authorize non admin user to only link a directory of files
Hi John, thanks for your reply, I'll give it a try. Thomas Von: John Chilton [jmchil...@gmail.com] Gesendet: Montag, 7. April 2014 16:15 An: Berner, Thomas Cc: galaxy-dev@lists.bx.psu.edu Betreff: Re: [galaxy-dev] authorize non admin user to only link a directory of files I think you need to hack up the Galaxy code to accomplish this. There is information on how to start doing this in the following thread I think: http://dev.list.galaxyproject.org/FTP-Problem-Users-cannot-see-their-uploads-files-tp4619709p4662701.html This may just work for admin users though, I don't recall. It is hopefully a helpful start though. -John On Mon, Apr 7, 2014 at 9:02 AM, Berner, Thomas thomas.ber...@jki.bund.de wrote: Hi, we recently activated the feature for non admin users which allows them to upload a directory of files: ... # Add an option to the library upload form which allows authorized # non-administrators to upload a directory of files. The configured directory # must contain sub-directories named the same as the non-admin user's Galaxy # login ( email ). The non-admin user is restricted to uploading files or # sub-directories of files contained in their directory. #user_library_import_dir = None user_library_import_dir = /opt/galaxy/galaxy-share/ ... However we would like to restrict the permission to only link to their files without copying them into galaxy, is this possible? Greetings, Thomas --- Thomas Berner Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants - Erwin Baur-Straße 27 06484 Quedlinburg - Germany - Phone: ++49 ( 0 ) 3946 47 562 EMail: thomas.ber...@jki.bund.de ___ 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] Can a tool upload a .loc file that is then reused by subsequent versions of the tool?
Hey folks! I'm trying to revise a tool that allows the user to select from an extendable list of template files for generating blast report output. The idea is that if some reporting needs aren't covered by a generic template, then they can develop their own template which can then show up on the list. And, wanting this to work with a tool that is versioned in the toolshed! So: 1) is there a way to include a .loc.sample in the tool that gets uploaded, and then can be manually revised over time? A .loc file that subsequent versions of the tool would reuse (instead of using their own minimal one that comes with toolshed install)? I can simply have the default template in the tools code folder, since it is apt to be upgraded over time. Custom reports would have their own absolute file paths defined in the .loc file. Thanks for your input! Damion ___ 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] Can a tool upload a .loc file that is then reused by subsequent versions of the tool?
Isn't this how *.loc.sample files already work? If there is no pre-existing *.loc file, the *.loc.sample file is copied to become the initial *.loc file which the local Galaxy administrator can update/fill in as needed. Peter On Mon, Apr 7, 2014 at 9:39 PM, Dooley, Damion damion.doo...@bccdc.ca wrote: Hey folks! I'm trying to revise a tool that allows the user to select from an extendable list of template files for generating blast report output. The idea is that if some reporting needs aren't covered by a generic template, then they can develop their own template which can then show up on the list. And, wanting this to work with a tool that is versioned in the toolshed! So: 1) is there a way to include a .loc.sample in the tool that gets uploaded, and then can be manually revised over time? A .loc file that subsequent versions of the tool would reuse (instead of using their own minimal one that comes with toolshed install)? I can simply have the default template in the tools code folder, since it is apt to be upgraded over time. Custom reports would have their own absolute file paths defined in the .loc file. Thanks for your input! Damion ___ 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] Can a tool upload a .loc file that is then reused by subsequent versions of the tool?
Oh, great! I'd assumed new tool versions would overwrite them so they could implement changes. But what you say is simpler and more straightforward! Thanks, D. From: Peter Cock [p.j.a.c...@googlemail.com] Sent: Monday, April 07, 2014 2:23 PM To: Dooley, Damion Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Can a tool upload a .loc file that is then reused by subsequent versions of the tool? Isn't this how *.loc.sample files already work? If there is no pre-existing *.loc file, the *.loc.sample file is copied to become the initial *.loc file which the local Galaxy administrator can update/fill in as needed. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Securing REMOTE_USER against local users
Galaxy admins, a couple questions:If you're running galaxy with REMOTE_USER authentication, do you have local users on the same box?If you do, have you done anything to mitigate administrator impersonation in galaxy?We currently have galaxy deployed on a box that acts as a classroom server. I was poking around and noticed that it was trivial to make curl requests with the REMOTE_USER variable set, and impersonate an admin. I've been considering solutions to this and arrived on the conclusion that the interface should require a "password" in addition to REMOTE_USER being set. That is, a header with a long random string should be required to be set in the reverse proxy configs, as well as being checked on the galaxy side much like how REMOTE_USER is checked. Thoughts?-- Eric RascheProgrammer IICenter for Phage TechnologyTexas AM UnivesityCollege Station, TX 77843Ph: 4046922048 ___ 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] visualization button
Hi Rudolph, Thanks for the answer. I understand that it would make no sense to allow generation of graphics on non relevant data. My data is in tabular format and that is the reason why I was surprise not to see that button. outputs data name=tabular_file label=report.tsv type=tabular format=tabular / /outputs I wouldn't be surprised if something was wrong in my syntax. Thanks for the help anyway. Cheers, Philip 2014-04-07 16:52 GMT+10:00 Hans-Rudolf Hotz h...@fmi.ch: Hi Philip The appearance of the visualization button depends on the datatype of your output. E.g. when it is set to 'tabular', you should get the button allowing you to create a scatter plot. However, depending on your data, it might not make much sense to visualize it in 'Trackster', 'Circster' or as scatter plot. Regards, Hans-Rudolf On 04/07/2014 02:11 AM, Philippe Moncuquet wrote: Hi, I have developed a simple script that give some statistics on an assemble. It generates a tabular output. The visualization button is not available when I extend the output in the history pane. Is there any code that I need to put in my xml wrapper to get this button available ? Regards, Philip ___ 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] krona to metaphlan patch
I’m running with these local additions to Dannon’s metaphlan repo.
I think it would be better to add these to the current metaphlan repo than to
release them standalone.
metaphlan_to_krona.xml
Description: metaphlan_to_krona.xml
#!/usr/bin/env python
# ==
# Conversion script: from MetaPhlAn output to Krona text input file
# Author: Daniel Brami (daniel.br...@gmail.com)
# ==
import sys
import optparse
import re
def main():
#Parse Command Line
parser = optparse.OptionParser()
parser.add_option( '-p', '--profile', dest='profile', default='', action='store', help='The input file is the MetaPhlAn standard result file' )
parser.add_option( '-k', '--krona', dest='krona', default='krona.out', action='store', help='the Krona output file name' )
( options, spillover ) = parser.parse_args()
if not options.profile or not options.krona:
parser.print_help()
sys.exit()
re_candidates = re.compile(rs__|unclassified\t)
re_replace = re.compile(r\w__)
re_bar = re.compile(r\|)
metaPhLan = list()
with open(options.profile,'r') as f:
metaPhLan = f.readlines()
f.close()
krona_tmp = options.krona
metaPhLan_FH = open(krona_tmp, 'w')
for aline in (metaPhLan):
if(re.search(re_candidates, aline)):
x=re.sub(re_replace, '\t', aline)
x=re.sub(re_bar, '', x)
x_cells = x.split('\t')
lineage = '\t'.join(x_cells[0:(len(x_cells) -1)])
abundance = float(x_cells[-1].rstrip('\n'))
metaPhLan_FH.write('%s\n'%(str(abundance) + '\t' + lineage))
metaPhLan_FH.close()
if __name__ == '__main__':
main()
Could they be integrated?Thanks!Brad
--Brad Langhorst, Ph.D.Applications and Product Development Scientist
___
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[galaxy-dev] patches to bjorn's bismark wrapper
This patch updates bjorn’s bismark wrapper to work with latest bismark and allows methylation extraction from SAM or BAM files. It no longer sorts the BAM from bismark (to allow methylation extraction to work). bismark_patch.diff Description: bismark_patch.diff Comments/corrections welcome.brad --Brad Langhorst, Ph.D.Applications and Product Development Scientist ___ 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] Check file before uploading
Hi When selecting a file or after clicking on Execute to upload a file is it possible to check the file is appropriate i.e. by checking file extension etc, before the file is actually uploaded and put into the database? So the user can't upload the wrong file/format Thanks Neil Neil Burdett Software Engineer | The Australian e-Health Research Centre Computational Informatics CSIRO E: neil.burd...@csiro.au T: 07 3253 3626 Address: Level 5, UQ Health Science Building 901/16 Royal Brisbane and Women's Hospital, Herston, Brisbane, QLD, 4029 www.csiro.au | http://milxview.csiro.au ___ 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/
