Mercurial to push changes to toolshed repo
by Joachim Jacob
Hi all,
As a test, I have uploaded some template files to a newly created
repository on our test toolshed. I pulled that repository on my
development machine using mercurial: from this folder I start now
developing the tool wrapper.
I have noticed that once the tool name has been set in the tool config
(<tool name="xxxxx" >) during the initial upload, pushing a subsequent
change to this name, this does not change the name on the repository
anymore (and the other settings, for this matter). Is this correct?
Thanks,
Joachim
--
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
10 years, 4 months
Best practice: set tool version on wrapper or on tool level?
by Joachim Jacob
Hi all,
I am writing a wrapper around Razers mapper. Currentty, Razers has three
versions, the latest being razers3.
Since it's under development, what is the best way to deal with new
versions?
- write a different tool config for every version, giving them different
ids like 'razers3', 'razers4'. These tools will appear all
simultaneously in the tool box. Every version needs to be installed
independently from the toolshed.
- or write a tool config with id 'razers' and set a version in the xml
<version_command>. Then when a new version comes out, I update the
wrapper completely to match the new version. In this way a user can
select the different versions can be selected at the top of the tool
parameters page in Galaxy, right? How should I deal with naming the
version: follow the config file I wrote (version 1.0.0 for razer3, 2.0.0
for razers4 - can cause confusion though.)
- or write a wrapper for the tool 'razers' in general, parsing the
selection of which version to use to the wrapper, and deal with it over
there?
I hope I explained my issue clearly.
Thanks,
Joachim
--
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
10 years, 4 months
[Patch] Interval error
by Björn Grüning
Hi,
for some strange gff files i get the following error:
Traceback (most recent call last):
File
"/media/data/web/galaxy-central/lib/galaxy/jobs/runners/local.py", line
149, in run_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/media/data/web/galaxy-central/lib/galaxy/jobs/__init__.py",
line 373, in finish
dataset.datatype.set_meta( dataset, overwrite = False ) #call
datatype.set_meta directly for the initial set_meta call during dataset
creation
File
"/media/data/web/galaxy-central/lib/galaxy/datatypes/interval.py", line
829, in set_meta
if valid_start and valid_end and start < end and strand in
self.valid_gff3_strand and phase in self.valid_gff3_phase:
UnboundLocalError: local variable 'start' referenced before assignment
start and end are not defined when elems[3] and elems[4] are '.'
Attached is a patch that should fix it.
Cheers,
Bjoern
10 years, 4 months
Renaming in Workflows
by Kohler Manuel
Hi,
I have workflows where I would like to rename the item at each step. The
reason for this to have a proper naming.
What I did is to use the renaming option in the workflow editor. I
specified the 'New output name:' to ${input}
This does not work.
Is there any variable which works or is there a easy way in doing this?
Any help or hint is appreciated.
Cheers
Manuel
--
Manuel Kohler
Center for Information Sciences and Databases (C-ISD)
Department of Biosystems Science & Engineering (D-BSSE)
ETH Zurich, Maulbeerstrasse (1078, 1.02), CH-4058 Basel, +41 61 387 3132
10 years, 4 months
Boolean logic in filters for data in outputs
by Oleksandr Moskalenko
Hi,
I am working on a wrapper that has multiple combinations of switches that lead to the creation of the output files. For instance, one of the files can be generated by conditions "A and B" and also by "A and C". FIrst, I tried the xml <and> and <or> elements, but that didn't work. Next, I tried having two <data> elements with the same name that contained those two pairs of filters. However, it appears that Galaxy only checks the last <data> element, which in this case is "A and C", so "A and B" is never triggered. In other cases there are three variables in play as the two main variables are not initialized if the advanced options conditional parameter's value is on. Passing the options to the wrapper is not a problem - only setting the outputs.
I pasted the complete tool definition file at http://pastebin.com/BGDzcc28.
Thanks,
Alex
10 years, 4 months
major database corruption
by Julian Pradinuk
Please help!
I'm new to sys admin and I've really messed up.
On our server we have a development instance and a production instance of
Galaxy. Both run under the same user (galaxy) and each has its own
postgresql table (galaxydb_dev and galaxydb_prod).
I was testing the ability to backup and restore with the development
instance but made the following huge mistake:
- ran "pg_dump galaxydb_dev 25_09_2012.sql"
- connected to the production instance database by accident
- ran "galaxydb_prod=# \i 25_09_2012.sql"
Is there any way that I can at least get the important relations and tuples
out and in to a new production instance? I have the dump file and the
output from running the \i command... Has anyone recovered from a similar
situation?
10 years, 4 months
cufflinks and global_model.txt
by wormbuff
I recently installed Galaxy on Ubuntu 12.04.1 LTS. Bowtie, SAMtools, and Tophat all run fine with my small subset of paired-end Illumina reads. Unfortunately, it seems to only partially work when I run Cufflinks v2.0.2.
Three entires in my history appear (gene expression, transcript expression, and assembled transcripts) containing reasonable output. Each of these entries is highlighted red, though without the red circle with an X. The box contains the message:
An error occurred running this job:
cufflinks v2.0.2
cufflinks -q --no-update-check -l 300000 -F 0.100000 -j 0.150000 -p 4
cp: cannot stat ` /home/galaxy/galaxy-dist/database/job_working_directory/000/20/global_model.txt':
No such file or directory
What is this global_model.txt file and why might it be missing/have failed?
(sorry about the repost... original got embedded in an unrelated thread)
10 years, 4 months
where are the tools?
by David Hoover
I just recently updated to the latest version of galaxy-central, and when
I started galaxy, the tools were not listed on the left panel. I could
rerun old jobs from my history, however. Why are the tools not listed?
David Hoover
Helix Systems Staff
10 years, 4 months
Stop Jobs
by Julian Pradinuk
Hi all,
I've been poking around with the Admin Manage jobs functions - Stop Jobs
does not seem to be working.
I looked at the code and added some debug prints. When I submit a Stop Jobs
in the manager, I don't think the job is making its way to the
stop_jobs_queue in the handler.... Are others having issues with this?
Is there a configuration I could be missing?
Cheers,
julian
10 years, 4 months
