upgrading my local galaxy install
by Erick Antezana
Hi,
I have upgraded my local install by getting the latest source like this:
hg pull -u
then I compared the *.sample.xml files against my *.xml files
(tool_conf.xml).
I have also upgraded my DB (from version 6 to 7).
I have also launched :
sh run_functional_tests.sh
and I got a message:
...
*** This program requires python version 2.5 or higher
*** Current python version is: 2.4.3.final.0
...
I have python 2.4.3. Do I need to upgrade it?
During the tests execution I saw the following error messages:
...
Test uploading encode data ... ERROR
...
...
Gencode Partition ( gencode_partition1 ) > Test-1 ... FAIL
...
Stitch MAF blocks ( Interval_Maf_Merged_Fasta2 ) > Test-1 ... FAIL
Stitch MAF blocks ( Interval_Maf_Merged_Fasta2 ) > Test-2 ... FAIL
...
Summary Statistics ( Summary_Statistics1 ) > Test-1 ... FAIL
...
BLAT ( blat_wrapper ) > Test-1 ... FAIL
...
Fetch taxonomic representation ( Fetch Taxonomic Ranks ) > Test-1 ... FAIL
Poisson two-sample test ( poisson2test ) > Test-1 ... FAIL
Poisson two-sample test ( poisson2test ) > Test-2 ... FAIL
Compute phastOdds score ( phastOdds_for_intervals ) > Test-1 ... FAIL
LAV to BED ( lav_to_bed1 ) > Test-1 ... FAIL
...
FAILED (failures=38, errors=5)
the rest are OK, some errors and failures I guess are due to the fact that I
do not have some tools installed (e.g. BLAT)
Do I need to perform any other operation in order to upgrate my local
install? (what about the "eggs"? Do I need to check for egg updates? how?)
thanks,
Erick
13 years, 3 months
Running gops_cluster.py on the command line fails
by Daniel Gerlach
Dear Galaxy Team,
I followed the instructions and downloaded the Galaxy distribution
according to the WIKI. As I do want to run some specific tools locally
on the shell, I put import sys and
sys.path.append("/somedir/galaxy/lib") before the galaxy module is loaded.
However the tool seems not to work and still gives me some errors which
I can not figure out. I'd be thankful for some ideas.
$ python /somedir/galaxy/tools/new_operations/gops_cluster.py
Traceback (most recent call last):
File
"/home/cegg/gerlach/bin/galaxy/tools/new_operations/gops_cluster.py",
line 22, in ?
from galaxy.tools.util.galaxyops import *
File "/home/cegg/gerlach/bin/galaxy/lib/galaxy/tools/__init__.py",
line 16, in ?
from galaxy.util.template import fill_template
File "/home/cegg/gerlach/bin/galaxy/lib/galaxy/util/template.py",
line 2, in ?
pkg_resources.require( "Cheetah" )
File "/home/cegg/gerlach/bin/galaxy/lib/galaxy/eggs/__init__.py",
line 544, in require
sys.path.remove(entry)
ValueError: list.remove(x): x not in list
With best regrads, Daniel
--
Daniel Gerlach, PhD student
Computational Evolutionary Genomics Group (CEGG)
email: daniel.gerlach(a)unige.ch
www: http://cegg.unige.ch/
13 years, 3 months
Join EST and Refseq
by Massimo
Hi,
I am trying to join a list of EST generated by UCSC Table (user track)
with all bovine Refseq list generated as well from UCSC. The two do not
share any common column and I cannot have the EST with the associated
Refseq. As suggested by people at UCSC I have generated my list of custom
track EST and then I have set the group mRNA and EST track, track mRNA,
Table RefSeq gene (reGene) and I have done an intersection with all my ESTs
(All refGene records that have any overlap with User Track ). I have then
send everything to Galaxy and try to use the join two queries feature but I
cannot obtain a unique table with both Refseq and EST accession numbers. I
have contacted the people from UCSC but they said that there is a way
through Galaxy..but I could not figured it out.
Please, let me know if there is a way.
Thanks in advance for your help!
Massimo Bionaz PhD
Post-doctoral researcher
Institute for Genomic Biology,
University of Illinois
366 Animal Sciences Laboratory
1207 W. Gregory Dr.
Urbana, IL 61801
USA
Office Tel: 1-217-333-6189
Fax: 1-217-333-8286
13 years, 3 months
string input contains "~"
by R
Hi,
My string type input includes "~", but I found galaxy turned it into "X", so my tool failed to run for the wrong input.
Does anyone know how to fix it?
Thanks!
13 years, 3 months
mapping
by Marcus Ludwig
Hi,
I want to map a set of sequences (derived from RNA) against a bacterial
genome. Unfortunately, the genome of Synechococcus sp. PCC 7002 consists
of one chromosome and six plasmids. In MAQ I can chose only one DNA
entry for mapping. In local BLAST it was possible to generate databases
consisting of several DNA entries to map the data.
Does anybody have experience in mapping transcription data against
complex genomes in Galaxy.
Best regards,
Marcus
13 years, 3 months
An idea for sharing tools
by James Casbon
Hi Everyone,
I have an "I want a pony" idea that I would like to kick onto the mailing list:
It would be great if there was a way for sharing tool definitions between users.
At the moment, the main repo is maintained by the galaxy team, and
that is fine and makes sense. However, I'm sure there is a lot of
duplicated work between the users when adding other tools in. For
example, there was a conversation the other day about adding in awk.
Someone had already done this, so the best idea would be if I could
pull in that definition and enable it with minimum effort. I have
already added tools (exonerate, restriction mapper, etc, etc) that may
be of use to other people. Not sure the best way to go about this,
but if my understanding of mercurial is right, we can simply offer
another repo for people to pull changes from.
If this is of interest to you, please can you reply? If we get enough
interest and preferably some support of the core team, I could set up
a free repo at, e.g., bitbucket and add users to it. Or perhaps there
is a better way (eg patches submitted to trac)? Another question is
what kind of tools would the core team accept for inclusion in the
main dist?
Cheers,
James
13 years, 3 months
Exception when using remote_user.
by MORITA Hideyuki
Hi,
The following error will occur under certain condition when using remote_user.
AttributeError: 'NoneType' object has no attribute 'user'
This error is thrown when:
1. using remote_user
2. browser has a valid session (cookie)
3. after logged in with an email address other than previously used
This is caused by None value in prev_galaxy_session variable at L.231 in
lib/galaxy/web/framework/__init__.py.
I understand that galaxy_session instead of prev_galaxy_session should be
referenced here.
I created a patch to fix this problem by replacing prev_galaxy_session with
galaxy_session.
===================================================================================
diff -r a4214de3752e lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py Tue Feb 03 18:34:27 2009 -0500
+++ b/lib/galaxy/web/framework/__init__.py Mon Feb 16 13:31:02 2009 +0900
@@ -228,7 +228,7 @@ class UniverseWebTransaction( base.Defau
invalidate_existing_session = True
user_for_new_session = self.__get_or_create_remote_user( remote_user_email )
log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session",
- remote_user_email, prev_galaxy_session.user.email )
+ remote_user_email, galaxy_session.user.email )
else:
# No session exists, get/create user for new session
user_for_new_session = self.__get_or_create_remote_user( remote_user_email )
===================================================================================
Thanks.
MORITA Hideyuki
13 years, 3 months
