Hey guys,
we know that we can use a variable to rename output files after their input e.g. #{input}, by using the "rename dataset" action in the workflow editor.
However, we would like to use these variable as a workflow parameter too, e.g. for the "Add or Replace Groups" tool as the ID tag, so the ID would be the dataset name.
Currently we have to specify read groups for 190 datasets and doing this manually would take a long time, so we would prefer to automatize it.
Is this possible?
Thanks for any advice.
Cheers, 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.berner(a)jki.bund.de
I'm doing a 1 step generic reporting tool along the lines of the "BLAST XML to tabular" script by Peter. I was just about to ask about this line, which looked pretty much like a bug:
sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(" >"))
Then I found the patch from Nov 7th 2013:
https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus...
try:
sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(" >"))
except IndexError as e:
stop_err("Problem splitting multuple hits?\n%r\n--> %s" % (hit_def, e))
Yay! But what I've seen in recent XML output reports is that the ">" content has been changed to ">" . E.g.
https://github.com/biopython/biopython/blob/master/Tests/Blast/mirna.xml
<Hit>
<Hit_num>66</Hit_num>
<Hit_id>gi|195029385|ref|XR_047134.1|</Hit_id>
<Hit_def>Drosophila grimshawi miR-7-RA (Dgri\mir-7), ncRNA >gi|195336156|ref|XR_048470.1| Drosophila sechellia miR-7-RA (Dsec\mir-7), ncRNA >gi|195585143|ref|XR_050309.1| Drosophila simulans miR-7-RA (Dsim\mir-7), ncRNA</Hit_def>
<Hit_accession>XR_047134</Hit_accession>
...
So perhaps a stop_err() could be avoided, if test is for ">" instead? I assume that no variants of python ElementTree.iterparse() will unescape content when returned via the iterator?
Damion
When a file is uploaded via FTP, and the file is compressed using gzip, the file is uploaded and decompressed on the fly; however, the gzipped file is left on the FTP server, rather than being deleted as normal. Is this a bug?
David Hoover
Helix Systems Staff
Hello, I would like to get a copy of the script that you use to convert tabular data to fasta files on the galaxy server. Would you mind sharing it with me?
Thanks!
Richard Hagan
Hi all,
I'm installing a new galaxy instance and run into an issue after switching to postgres. During the migration setps I get the following error
galaxy.model.migrate.check INFO 2013-11-21 15:37:23,238
galaxy.model.migrate.check INFO 2013-11-21 15:37:23,238 Migrating 103 -> 104...
galaxy.model.migrate.check INFO 2013-11-21 15:37:23,257
galaxy.model.migrate.check INFO 2013-11-21 15:37:23,257 Migrating 104 -> 105...
galaxy.model.migrate.check INFO 2013-11-21 15:37:25,413
galaxy.model.migrate.check INFO 2013-11-21 15:37:25,414 Migration script to add the cleanup_event* tables.
galaxy.model.migrate.check INFO 2013-11-21 15:37:25,414
galaxy.model.migrate.check INFO 2013-11-21 15:37:25,414
galaxy.model.migrate.check INFO 2013-11-21 15:37:25,414 Migrating 105 -> 106...
galaxy.model.migrate.check INFO 2013-11-21 15:37:25,414
Traceback (most recent call last):
File "/mnt/data/home/NIOO/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/mnt/data/home/NIOO/galaxy/galaxy-dist/lib/galaxy/app.py", line 54, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self )
File "/mnt/data/home/NIOO/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 66, in create_or_verify_database
migrate_to_current_version( engine, db_schema )
File "/mnt/data/home/NIOO/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 124, in migrate_to_current_version
schema.runchange( ver, change, changeset.step )
File "/mnt/data/home/NIOO/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/schema.py", line 89, in runchange
(self.version, startver))
InvalidVersionError: 103 is not 105
./manage_db.sh upgrade
seems to finish the migration.
How do I ensure the database is in a healthy state?
Ubuntu 12.04.3 LTS
PostgreSQL 9.1
Connection via socket
Installation as local galaxy user
Installation started in virtual environment
Victor
I'm working with a lot of data on a cluster (condor). If I save all the
workflow intermediate data, as Galaxy does by default (and rightfully so),
it fills the drives.
How can tell Galaxy to use /tmp/ to store all intermediate data in a
workflow, and keep the result?
I imagine I'll have to work on how Galaxy handles jobs, but I'm hoping
there is something built in for this.
Thanks
Hi,
I found that the GATK tools do not have the same requirement tag. For
example indel-realigner has version 1.4, realigner_target_creator has
version 1.3. Is that correct? What is the recent version that is
required for GATK?
Also realigner_target_creator uses the "gatk_picard_indexes" location
file, but under tool-data is only a gatk_sorted_picard_indexes.loc
file.
Are there any concrete plans for the GATK wrappers. Especially to update
to a newer version. Or is that not feasible because of this complicated
license policy and the phone-home option ...
I found the following trello card, but its a little bit outdated:
https://trello.com/c/IPkT2spd
Is anyone running a recent GATK version in Galaxy?
Thanks!
Bjoern
Hello all,
It is my recollection that under the "Admin" panel, "Manage jobs"
page, there used to be a toggle control to lock the submission
of new jobs. This was very helpful in preparation for scheduling
a system shutdown (e.g. for hardware or software updates).
However, I no longer see this option on either galaxy-central
or galaxy-dist. Was it removed, or am I imagining things - in
which case should I file an enhancement request ;)
(I've had a look in Trello and didn't find anything)
Thanks,
Peter
Woops - I realize now findtext() must be unescaping all ">", so Peter was trying to address other non-splitting occurances of " >" as per his patch notes. But perhaps a stop_err() isn't merrited in this case?
So ignore my test for ">" comment.
Regards,
Damion
Hi,
I would like to inquire whether anyone has attempted to implement the
idxstats tool from samtools into Galaxy?
The xml-file for idxstats is not present in the Galaxy source code,
which led me to try and implement it myself.
However, the main problem I face is that the idxstats tool silently
relies on having an index file available (within the same directory)
for the bam file you which to print the stats for.
E.g.
samtools idxstats PATH/test.bam
searches for PATH/test.bam.bai and gives an error when this file is not
present. And somehow I cannot model this behavior in Galaxy.
A different solution would of course be to ask the author(s) of samtools
to have an option available where the user can directly indicate the
path to the index file.
regards,
Michiel
PS: I've searched the mailing list archives for this problem but did not
find any matches. Apologies if I somehow missed the answer.
--
==================================================================
Michiel Van Bel, PhD
Expert Bioinformatician
Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
mibel(a)psb.vib-ugent.be http://www.psb.vib-ugent.behttp://bioinformatics.psb.ugent.be
==================================================================
