Command Line Tool for Creating New Users
by Adam Brenner
Howdy All,
I was wondering if anyone has created a command line tool that will
add users to the Galaxy user database?
I did look into switching to external user authentication via nginx,
however, this will result in us using the campus wide kerberos system
and allowing ~30,000 people access to Galaxy... and thus offering us
less fine grain control to Galaxy.
Anything anyone has to share would be much appreciated,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebrenne(a)uci.edu
9 years, 9 months
Running Galaxy through Apache
by Jeffrey Long
Hi folks,
I am wanting to run a galaxy instance and serve it at a location other than
the webserver root, i.e. at http://mymachine.com/galaxy rather than just
at http://mymachine.
To do this, I've followed the instructions about proxying Galaxy through
Apache at http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy. I'm
pretty sure I've followed the instructions exactly. I enabled the
necessary apache proxy modules and then I added these lines to my
apache.conf file:
RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule^/galaxy/static/style/(.*)
/myplace/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule^/galaxy/static/scripts/(.*)
/myplace/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule^/galaxy/static/(.*)
/myplace/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico
/myplace/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt
/myplace/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*)
http://localhost:8080$1 [P]
...and re-started the apache server without a problem (note: I also tried
it commenting out everything but the first, second and last line in case
there was an issue with the static stuff).
I then made sure the following lines were present and uncommented in my
universe_wsgi.ini file
[filter:proxy-prefix]use = egg:PasteDeploy#prefixprefix =
/galaxy[app:main] filter-with = proxy-prefixcookie_path = /galaxy
I start up Galaxy. And still, I can only reach it on http://mymachine:8080,
not at http://mymachine/galaxy as I intend.
Any help would be appreciated! Thanks!
-Jeff
9 years, 9 months
Environment variables
by Matthias Zytnicki
Dear everyone,
I have spent hours trying to set environment variable in Galaxy. I am
managing the "s_mart" repos (you can check it if you wish), and I created
the simple files "test.xml" which prints the environment variables:
---
<tool id="test" name="test">
<description>This is a test.</description>
<requirements>
<requirement type="set_environment">PYTHONPATH</requirement>
</requirements>
<command>env > $outputFile</command>
<outputs>
<data name="outputFile" format="txt" label="output test
file"/>
</outputs>
<help>This is a test.</help>
</tool>
---
and "tool_dependencies.xml", which appends something to the PYTHONPATH
variable.:
---
<?xml version="1.0"?>
<tool_dependency>
<set_environment version="1.0">
<environment_variable name="PYTHONPATH"
action="append_to">$REPOSITORY_INSTALL_DIR</environment_variable>
</set_environment>
</tool_dependency>
---
As you guess, I cannot see anything added in the PYTHONPATH variable. I
have tried to append INSTALL_DIR and even "/tmp". None worked.
Do you have any suggestion for me?
Many thanks to you all,
Matthias.
9 years, 9 months
/bin/sh: 1: filename: not found
by Ramon Tiburski
I created a new tool in c++, and the "filename" is the name of my executable file. I have the xml and the executable file in the same directory, but I get this error when I try to run the tool. Someone can help me with this error?
Thank you
9 years, 9 months
Speed up the galaxy
by 泽 蔡
Hi all,
How can I speed up the galaxy? Like how to use more cores and memeries.
9 years, 9 months
Re: [galaxy-dev] TestToolShed out of date? (not running unit tests)
by Peter Cock
On Wed, Apr 24, 2013 at 10:12 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
>
> ..., I've still finding some other cases where despite having
> tests defined, nothing shows up on the Tool Shed test results page.
>
> Here's an example where I see that two tools (promoter2 and
> wolf_psort) have no tests, but the results of all the other tools
> in this suite are not mentioned (some expected to fail/be skipped
> due to missing dependencies):
>
> http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
> Revision 13:dc958c2a963a
>
> Equivalently:
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
> Revision: 14:0d8b1d20ce9c
>
> --------------------------------------------------------------------------------
>
> Here's another example where based on what happens locally,
> I am expecting a failure:
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename
> Revision: 1:6ce8634e2035
>
> This is failing for me locally, but again I suspect this is due to an
> issue in the framework - much like the blastxml_to_top_descr
> test is failing due to the datatypes not being updated, here there
> seems to be something similar going wrong regarding the
> second uploaded input file (which is used for to provide the
> potential column parameters). See this thread:
>
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003867.html
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014261.html
>
> Regards,
>
> Peter
Hi Dave,
Yet another case,
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
Revision: 8:1f546099212f
and,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
Revision: 5:d42346e675c4
These list five or six invalid tools which do not define any unit
tests, yet there is no mention of the tools present which do have
tests (and if they passed or not).
Even if ncbi_blastdbcmd_wrapper doesn't (yet) have a test,
I still want to know if the ncbi_blastp_wrapper tests pass ;)
Are this further symptoms of whatever was solved here?
https://trello.com/card/toolshed-automated-functional-test-bug/506338ce32...
Or does would a new Trello issue be best?
Thanks,
Peter
9 years, 9 months
Merging files: Error merging filesglobal name 'shutil' is not defined
by Peter Cock
Hi all,
While testing a BLAST search using plain text output (the 'txt'
datatype in Galaxy) or subclasses (like 'blastxml') using galaxy-dist
with task splitting enabled, I found I new bug when the files are
merged:
Error merging files global name 'shutil' is not defined
This is a side effect of this commit due to a missing import
(perhaps the imports changed since Bjoern wrote the patch):
https://bitbucket.org/galaxy/galaxy-central/commits/510b063792de89332428e...
In addition to the missing import in data.py, there is a potential
similar issue with binary.py but this is masked by an evil
import * line ;)
My suggested patch for the import issue below, however right
now even though the merge is failing, Galaxy failed to treat
the job as a failure - it was shown as a green successful job
with "Error merging files" as stdout, and for stderr:
"global name 'shutil' is not defined", but return code 0.
So there is a deeper problem with the merge error not marking
the job as failed.
Also there is a minor bug in that the stdout and stderr are
combined for the peep text without any white space -
presumably most of the time the stdout will have a trailing
new line, but not here - thus "filesglobal" [sic], not say
"files global" or a newline. There's a second patch below
for that minor issue too (although it seems my new lines
get turned into spaces by the time they are shown in
the history peep text).
Regards,
Peter
--
$ hg diff
diff -r 8b9ca63f9128 lib/galaxy/datatypes/binary.py
--- a/lib/galaxy/datatypes/binary.py Wed Apr 24 16:24:41 2013 -0400
+++ b/lib/galaxy/datatypes/binary.py Thu Apr 25 11:32:51 2013 +0100
@@ -12,7 +12,7 @@
from bx.seq.twobit import TWOBIT_MAGIC_NUMBER,
TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE
from urllib import urlencode, quote_plus
import zipfile, gzip
-import os, subprocess, tempfile
+import os, subprocess, tempfile, shutil
import struct
log = logging.getLogger(__name__)
diff -r 8b9ca63f9128 lib/galaxy/datatypes/data.py
--- a/lib/galaxy/datatypes/data.py Wed Apr 24 16:24:41 2013 -0400
+++ b/lib/galaxy/datatypes/data.py Thu Apr 25 11:32:51 2013 +0100
@@ -3,6 +3,7 @@
import mimetypes
import os
import sys
+import shutil
import tempfile
import zipfile
from cgi import escape
$ hg diff
diff -r 8b9ca63f9128 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py Wed Apr 24 16:24:41 2013 -0400
+++ b/lib/galaxy/jobs/__init__.py Thu Apr 25 11:43:30 2013 +0100
@@ -924,7 +924,13 @@
for dataset in
dataset_assoc.dataset.dataset.history_associations +
dataset_assoc.dataset.dataset.library_associations: #need to update
all associated output hdas, i.e. history was shared with job running
dataset.blurb = 'done'
dataset.peek = 'no peek'
- dataset.info = ( dataset.info or '' ) +
context['stdout'] + context['stderr']
+ dataset.info = (dataset.info or '')
+ if context['stdout'].strip():
+ #Ensure white space between entries
+ dataset.info = dataset.info.rstrip() + "\n" +
context['stdout'].strip()
+ if context['stderr'].strip():
+ #Ensure white space between entries
+ dataset.info = dataset.info.rstrip() + "\n" +
context['stderr'].strip()
dataset.tool_version = self.version_string
dataset.set_size()
if 'uuid' in context:
9 years, 9 months
traceback - local error?
by Langhorst, Brad
172.17.130.203 - - [19/Apr/2013:10:31:20 -0400] "GET /api/datasets/dd61915e24aa3fd0?hda_ldda=hda&data_type=converted_datasets_state&chrom=chr1 HTTP/1.1" 200 - "http://galaxy.neb.com/visualization/trackster?dataset_id=b8edc02014d74add..." "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_3) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.65 Safari/537.31"
galaxy.webapps.galaxy.api.datasets ERROR 2013-04-19 10:31:21,775 Error in dataset API at listing contents: unpack requires a string argument of length 4: unpack requires a string argument of length 4
Traceback (most recent call last):
File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 41, in show
is_true( kwd.get( 'retry', False ) ) )
File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 96, in _converted_datasets_state
if not data_provider.has_data( chrom ):
File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 1037, in has_data
f, bbi = self._get_dataset()
File "/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 1170, in _get_dataset
return f, BigWigFile(file=f)
File "bigwig_file.pyx", line 127, in bx.bbi.bigwig_file.BigWigFile.__init__ (lib/bx/bbi/bigwig_file.c:3011)
File "bbi_file.pyx", line 119, in bx.bbi.bbi_file.BBIFile.__init__ (lib/bx/bbi/bbi_file.c:3508)
File "bbi_file.pyx", line 129, in bx.bbi.bbi_file.BBIFile.open (lib/bx/bbi/bbi_file.c:3660)
File "/mnt/ngswork/galaxy/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg/bx/misc/binary_file.py", line 30, in __init__
if struct.unpack( ">I", bytes )[0] == magic:
error: unpack requires a string argument of length 4
Is this a bug or have I done something unexpected?
I'm trying to use the trackbrowser to visualize some bam files that I aligned to a genome that I had to install manually (Zea_mays_B73_RefGen_v2), maybe i've screwed something up.
I was initially able to see some reads, but after reverting to the sample datatypes file and restarting galaxy i can't see anything anymore.
I also added a .2bit file to twobit.locs
Zea_mays_AGPv2 /mnt/ngswork/galaxy/galaxy-dist/tool-data/genome/Zea_mays_AGPv2/seq/Zea_mays_AGPv2.2bit
maybe that's related...
I've tried copying the bams to a new history - and they seem to be reindexing as a result, but I still see no reads.
Any ideas?
Brad
--
Brad Langhorst
langhorst(a)neb.com<mailto:langhorst@neb.com>
9 years, 9 months
Blast Errors
by Ganote, Carrie L
Hi list,
I installed the latest toolshed NCBI Blast+ into a new Galaxy and I'm trying to pinpoint these errors:
9 years, 9 months
