[galaxy-dev] Metadata in Galaxy Tool Shed

2011-07-22 Thread Lance Parsons
? Also, any suggestions on how to organize the files in the repository are welcome. Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University attachment

[galaxy-dev] Dataset Cleanup Question

2011-08-25 Thread Lance Parsons
days (and counting). I have even tried running the scripts with the -f option to force galaxy to re-evaluate the datasets to no avail. Any suggestions? Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton

[galaxy-dev] VCF 4.1 support

2011-09-01 Thread Lance Parsons
that you have, please let me know and I'll make sure that I address these. Al Is anyone working on modifying Galaxy to use the new vcfCTools? I would be willing to lend my support to such an effort. If not, is there at least support from the Galaxy team for doing this? -- Lance Parsons

[galaxy-dev] Bug importing from data library to history

2011-09-27 Thread Lance Parsons
(and the number of datasets does not change in the saved histories view). Any thoughts on what might be going on here? Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

Re: [galaxy-dev] MergeSamFiles.jar and TMPDIR

2011-10-03 Thread Lance Parsons
___ 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/ -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory

Re: [galaxy-dev] MergeSamFiles.jar and TMPDIR

2011-10-03 Thread Lance Parsons
The patches have been put into a pull request. Lance Nate Coraor wrote: Lance Parsons wrote: For what it's worth, I ran into an issue with the use of /tmp as well. When merging a lot of BAM files, /tmp filled up and the merge failed. To make matters worse, since STDERR is redirected

Re: [galaxy-dev] Bug importing from data library to history

2011-10-05 Thread Lance Parsons
: Lance Parsons wrote: I'm running a local instance of Galaxy that has been working quite well. However, I've recently run into a problem when importing datasets from a data library into a history. The Size on Disk of the history grows by the size of the imported dataset, however, the new dataset

Re: [galaxy-dev] Bug importing from data library to history

2011-10-05 Thread Lance Parsons
the copied HistoryDatasetAssociation is created, and whether the source LibraryDatasetDatasetAssociation is itself deleted (which should be the only way the resulting hda could be deleted). Lance Lance Parsons wrote: Good catch, that does indeed seem to be the issue. And it only seems to happen

Re: [galaxy-dev] Bug importing from data library to history

2011-10-05 Thread Lance Parsons
: select * from library_dataset where deleted=f and purged=t; With those, I would think setting purged to f and then setting deleted = f for the associated library_dataset_dataset_association records. Lance Nate Coraor wrote: Lance Parsons wrote: Good catch, that does indeed seem

Re: [galaxy-dev] Dataset Cleanup Question

2011-11-17 Thread Lance Parsons
issues (perhaps the datasets/histories were shared?)? If this issue is still open, there are new features in Galaxy to help manage data that may be of interest: http://galaxyproject.org/wiki/Admin/Disk%20Quotas Thanks! Jen Galaxy team On 8/25/11 9:16 AM, Lance Parsons wrote: I am running

[galaxy-dev] Display VCF in IGV problem

2011-12-05 Thread Lance Parsons
/princetonhtseq/tutorials/visualization-with-galaxy-and-igv/igv-as-a-display-application-in-galaxy). However, I can't figure out why BAM files work and VCF files don't. Any advice or insight would be appreciated. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler

[galaxy-dev] Tool Requirement tag and dependency management

2012-04-09 Thread Lance Parsons
do something like: requirements requirement type=packagebedtools/requirement requirement type=binarygenomeCoverageBed/requirement /requirements Secondly, once this is sorted out, it would be nice to update the Tool Config Syntax documentation. Thanks in advance for any advice. -- Lance

Re: [galaxy-dev] BAM to BigWig (and tool ID clashes)

2012-04-19 Thread Lance Parsons
, and the Python library pysam. Lance, your tool doesn't seem to include any author information like your name or email address. I'm inferring it is yours from the Galaxy tool shed user id, lparsons. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute

Re: [galaxy-dev] BAM to BigWig (and tool ID clashes)

2012-04-20 Thread Lance Parsons
file to match and add the new split option. We could list this as three contributing authors if you both like? Peter -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

[galaxy-dev] FreeBayes bug - update to a toolshed tool wrapper

2012-08-30 Thread Lance Parsons
/lance_parsons/freebayes/) and given Daniel and Greg access to it in hopes that would make things easier.Let me know if there is a better way to coordinate, etc. Thanks again. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics

Re: [galaxy-dev] FreeBayes bug - update to a toolshed tool wrapper

2012-08-31 Thread Lance Parsons
to 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf, with mostly minor differences from your pull request. Please let us know if you experience any issues installing or using the updated version (0.0.3). Thanks, Dan On Aug 30, 2012, at 11:35 AM, Lance Parsons wrote: I have been using

Re: [galaxy-dev] FreeBayes bug - update to a toolshed tool wrapper

2012-08-31 Thread Lance Parsons
). Thanks for using Galaxy, Dan On Aug 31, 2012, at 11:47 AM, Lance Parsons wrote: Thanks for the quick turnaround Dan. Much appreciated. When I tried to test updating Freebayes from the toolshed, I get a message that no updates are available. Perhaps it takes some time before

[galaxy-dev] Automatic installation of third party dependancies

2012-09-04 Thread Lance Parsons
) gets executed during installation. 2) Another issue is the inability to install Numpy as a dependancy to HTSeq. I can get Numpy to install, but it won't be in the PYTHONPATH when HTSeq is installed (or executed). Any thoughts on how to address these issues would be appreciated. -- Lance

Re: [galaxy-dev] FreeBayes bug - update to a toolshed tool wrapper

2012-09-11 Thread Lance Parsons
for the inconvenience on this. Greg Von Kuster On Aug 31, 2012, at 3:59 PM, Lance Parsons wrote: Thanks for the explanation. That makes sense. I went ahead and installed the new version along with dependencies in my development environments and all went well. Then in production, the installation

[galaxy-dev] FreeBayes Installation Bug

2012-09-11 Thread Lance Parsons
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 diff --git a/tool_dependencies.xml b/tool_dependencies.xml

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-11 Thread Lance Parsons
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

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-12 Thread Lance Parsons
-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

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-13 Thread Lance Parsons
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

[galaxy-dev] Tophat2 Issues

2012-09-14 Thread Lance Parsons
things a bit more robust, I suggest adding bowtie2 as a requirement to the tophat2 wrapper. It also might be a good idea to add versions to those requirements. I've attached a small patch to do that (though it's fairly trivial). Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-21 Thread Lance Parsons
... On Sep 13, 2012, at 4:41 PM, Lance Parsons wrote: Actually, I think that is exactly the issue. I DO have 3:f7a5b54a8d4f installed. I've run into a related issue before, but didn't fully understand it. I believe what happened was: 1) I pushed revision 3:f7a5b54a8d4f to the tool shed which

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-21 Thread Lance Parsons
from Mercurial (even version 2.3.3) do not seem to trigger metadata refreshes in the tool shed, however, uploads of tar.gz files do. Hope this helps. Lance Lance Parsons wrote: I've run into this issue again, and I'm having a hard time working around it. However, I have confirmed that at least

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-25 Thread Lance Parsons
; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Hope this helps. Lance Lance Parsons wrote: I've run into this issue again, and I'm having a hard time working around it. However, I have confirmed that at least some updates to a tool in the tool shed will invalidate previously

Re: [galaxy-dev] Automatic installation of third party dependancies

2012-09-27 Thread Lance Parsons
AM, Lance Parsons wrote: I'm sorry I wasn't more clear. I do believe that those links explain the behavior I am seeing. However, let me try to describe it a different way. It seems that there will, at most, be one installable revision of a given version of a tool. Here I use revision to denote

Re: [galaxy-dev] How to rotate Galaxy log file

2012-10-01 Thread Lance Parsons
___ 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/ -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute

Re: [galaxy-dev] Cannot install ncbi_blast_plus or other tools from Tool Shed: HTTP 500 error

2012-10-10 Thread Lance Parsons
/ ___ 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/ -- Lance Parsons - Scientific Programmer 134 Carl C

[galaxy-dev] Updating help text for a tool shed repository

2012-12-10 Thread Lance Parsons
have installed (10) is not longer considered a valid revision by the toolshed (I presume since it is an older revision of with the same tool version). Any help would be appreciated. Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute

Re: [galaxy-dev] Updating help text for a tool shed repository

2012-12-13 Thread Lance Parsons
describe above, we'll need more details as to the process you used in order to determine the cause of the problem. Greg Von Kuster On Dec 10, 2012, at 1:45 PM, Lance Parsons wrote: I recently updated the htseq-count tool in the Galaxy toolshed to version 0.3. This version has some functional

Re: [galaxy-dev] Updating help text for a tool shed repository

2012-12-17 Thread Lance Parsons
running mercurial version 2.2.3 and Python 2.5. What's your environment? Greg Von Kuster On Dec 13, 2012, at 2:30 PM, Lance Parsons wrote: Since I've had issues with workflow and the toolshed in the past, I have changed my workflow so that my only interaction with the toolshed is either

[galaxy-dev] Bug in handling user job limits

2013-01-11 Thread Lance Parsons
of `handler.py` is only called when jobs are tracked in the database. If jobs are not tracked in the database (as in my case), the error occurs. Perhaps the fix would be to simply move the call outside the `if` block. It appears this was broken in the 2012-11-13 revision (73e05bc). -- Lance Parsons

Re: [galaxy-dev] Bug in handling user job limits (due to dynamic job runner code?)

2013-01-18 Thread Lance Parsons
outside of the if block, does indeed fix that issue 2) Fixing that leads the __check_user_jobs method to fail since it does not check `self.track_jobs_in_database`, but instead assumes that jobs are in the database, resulting in a different exception regarding invalid columns. Lance Parsons wrote

Re: [galaxy-dev] Bug in handling user job limits (due to dynamic job runner code?)

2013-01-25 Thread Lance Parsons
of it committed (including this fix) some time this week. Thanks for figuring out exactly what's going on here. --nate On Jan 18, 2013, at 5:28 PM, Lance Parsons wrote: Just an update on this issue. Upon further investigation, it looks like the dynamic job runner code in commit 6f3b4e8 broke this. I

Re: [galaxy-dev] Galaxy: Dependency error htseq_count

2013-03-05 Thread Lance Parsons
will make it again a little closer to a perfect world :-) Cheers, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 12/17/2012 05:28 PM, Lance Parsons wrote: Thanks for looking

Re: [galaxy-dev] Galaxy: Dependency error htseq_count

2013-03-11 Thread Lance Parsons
Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 12/17/2012 05:28 PM, Lance Parsons wrote: Thanks for looking into this Greg. The environment where I'm having this problem is our testing

[galaxy-dev] Improving Administrative Data Clean Up (pgcleanup.py vs cleanup_datasets.py)

2013-03-22 Thread Lance Parsons
, logging, etc. Any tips on generally acceptable (supported) procedures for marking a dataset as deleted? Of course, I'll make any of the enhancements available (and would be happy to submit pull requests if there is interest). -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn

Re: [galaxy-dev] Galaxy: Dependency error htseq_count

2013-03-22 Thread Lance Parsons
Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 03/11/2013 06:34 PM, Lance Parsons wrote: I have posted an updated version of the htseq-count tool in the toolshed that uses and updated version of the HTSEQ count package (0.5.4p1

[galaxy-dev] Toolshed - Installation of static files

2013-03-22 Thread Lance Parsons
.. 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

Re: [galaxy-dev] Toolshed - Installation of static files

2013-03-22 Thread Lance Parsons
file ) .. image:: ./static/images/count_modes.png :width: 500 I believe that's all that is necessary. Greg Von Kuster On Mar 22, 2013, at 12:44 PM, Lance Parsons wrote: For one of my tool wrappers (htseq-count) in the toolshed, I point to an image file in the Help section

Re: [galaxy-dev] Improving Administrative Data Clean Up (pgcleanup.py vs cleanup_datasets.py)

2013-03-22 Thread Lance Parsons
Nate Coraor wrote: On Mar 22, 2013, at 11:56 AM, Lance Parsons wrote: I have been running a Galaxy server for our sequencing researchers for a while now and it's become increasingly successful. The biggest resource challenge for us has been, and continues to be disk space. As such, I'd like

[galaxy-dev] Bowtie2 and Tophat2 versions

2013-04-10 Thread Lance Parsons
that are compatible. 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

Re: [galaxy-dev] Improving Administrative Data Clean Up (pgcleanup.py vs cleanup_datasets.py)

2013-04-17 Thread Lance Parsons
by the update_time. I think files should be deleted by the access time. Is it enough to resolve this problem by checking the update_time of the HistoryDatasetAssociation table? Thanks for your help, X. Meng Joint Genome Institute, LBNL quote author='Lance Parsons' Nate Coraor wrote: On Mar 22

Re: [galaxy-dev] Tools declaring Python dependencies

2013-04-18 Thread Lance Parsons
/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

Re: [galaxy-dev] Improving Administrative Data Clean Up (pgcleanup.py vs cleanup_datasets.py)

2013-04-18 Thread Lance Parsons
Template Variables: cutoff - the cutoff in days email - the users email address datasets - a list of tuples containing 'dataset' and 'history' names Lance Parsons wrote: Nate Coraor wrote: On Mar 22, 2013, at 11:56 AM, Lance Parsons wrote: I have been running a Galaxy server for our

Re: [galaxy-dev] Galaxy hg repository problem abort: path ... traverses symbolic link

2013-04-29 Thread Lance Parsons
/mailinglists/ -- 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

Re: [galaxy-dev] Issue with set_user_disk_usage.py and Postgres 8.x

2013-06-06 Thread Lance Parsons
RETURNING disk_usage; -- 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

Re: [galaxy-dev] Issue with set_user_disk_usage.py and Postgres 8.x

2013-06-06 Thread Lance Parsons
No problem, glad it was helpful. Dannon Baker wrote: Thanks for the bug fix, (and for the reminder that it was still sitting in the inbox, sorry about that). I've verified the fix as well and pulled it into -central. -Dannon On Thu, Jun 6, 2013 at 10:13 AM, Lance Parsons lpars

[galaxy-dev] Toolshed bug related to readme files

2013-06-11 Thread Lance Parsons
error: http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=picardowner=devteamchangeset_revision=e0232cbac965 Looks like this changeset is relevant: https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac5e17ec5c9aaece023b0ae74db696 -- Lance Parsons - Scientific Programmer

Re: [galaxy-dev] Toolshed bug related to readme files

2013-06-11 Thread Lance Parsons
it once I get a chance tomorrow. --  Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University Original message From: Greg Von Kuster g...@bx.psu.edu Date: 06/11/2013 10:00 PM (GMT-05:00

[galaxy-dev] Toolshed Collaboration Issues

2013-10-02 Thread Lance Parsons
an issue on Trello (https://trello.com/c/XYkqW3Lr). -- 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

Re: [galaxy-dev] Toolshed Collaboration Issues

2013-10-02 Thread Lance Parsons
submitted an issue on Trello (https://trello.com/c/XYkqW3Lr). -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ Please keep all replies on the list

Re: [galaxy-dev] installing htseq-count from tool-shed

2014-06-10 Thread Lance Parsons
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/ -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn

[galaxy-dev] tool_data_table_conf.xml entries for migrated tools

2014-06-23 Thread Lance Parsons
for each migrated tool? Thanks for any help or suggestions. -- 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

[galaxy-dev] Updated Freebayes Wrapper - Bugs

2014-06-25 Thread Lance Parsons
these. Is there a bitbucket repo somewhere to submit pull requests? -- 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

[galaxy-dev] Updated Freebayes Wrapper (0.9.14) - Bug Report

2014-06-26 Thread Lance Parsons
these. Is there a bitbucket repo somewhere to submit pull requests? Also, I'm not sure if this is best sent to this list or put into Trello, etc. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

[galaxy-dev] Adding Reference Genomes, builds.txt vs manual_builds.txt

2014-08-04 Thread Lance Parsons
practice for adding a new genome? Updating builds.txt or manual_builds.txt? 2) Can the manual_builds.txt file be generated from a sample and moved out of source control? (I'll add a Trello card if this seems reasonable). -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory

[galaxy-dev] Jobs stuck in new state - Data Library datasets to blame?

2014-10-01 Thread Lance Parsons
was not ready for use as a job input? I'd very much like to fix these datasets since having to re-upload data libraries would be very tedious. Thanks in advance. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton

Re: [galaxy-dev] Jobs stuck in new state - Data Library datasets to blame?

2014-10-02 Thread Lance Parsons
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Aaron Petkau *Sent:* Wednesday, October 01, 2014 5:32 PM *To:* Lance Parsons *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] Jobs stuck in new state - Data Library datasets to blame? Are you attempting to upload datasets to a Data

[galaxy-dev] Apache proxy, SSL, and UCSC get data

2014-10-07 Thread Lance Parsons
https to the httpd.conf and that appears to be working. Is there something else I need to do? Should I patch the data_source tools to use https in the xml tool definitions? Thanks for any advice. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute

Re: [galaxy-dev] Jobs stuck in new state - Data Library datasets to blame?

2014-11-06 Thread Lance Parsons
. Thanks in advance. Lance Lance Parsons wrote: Thanks, that was the first thing I checked. However, restarting the handler didn't help. Downloading the offending data and re-uploading as a new data set and then rerunning using the new dataset as input did work. Also, all other jobs continued

[galaxy-dev] Is release_2014.10.06 official?

2014-11-11 Thread Lance Parsons
, I need to do to prepare for this update? 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

Re: [galaxy-dev] Jobs stuck in new state - Data Library datasets to blame?

2014-11-14 Thread Lance Parsons
latest_2014.08.11. Thanks in advance. Lance Lance Parsons wrote: Thanks, that was the first thing I checked. However, restarting the handler didn't help. Downloading the offending data and re-uploading as a new data set and then rerunning using the new dataset as input did work. Also, all other jobs