Re: [galaxy-user] Searching Galaxy Tool Shed gives error
Hello Joachim, Thanks for reporting this. This issue was resolved a couple of weeks ago, but did not make it into the cutoff for the last Galaxy distribution release. It is corrected on the test Galaxy tool shed and will be included in the next Galaxy release. Greg Von Kuster On Dec 12, 2012, at 4:52 AM, Joachim Jacob wrote: Hello, Searching the Galaxy toolshed for workflows on http://toolshed.g2.bx.psu.edu/ gives an error Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Cheers 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 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Bismark Error: Data table named 'bismark_bs_indeces' is required by tool but not configured.
Hello Sachit, It looks like you installed this from the test tool shed since it is not available on the main tool shed. Assuming I've located the repository you installed, it looks like you'll have to manually add the following entry into your tool_data_table_conf.xml file. This should have been done automatically for you when you installed the repository, but I'm not sure why it didn't. Maybe you're running an older version of Galaxy that doesn't include this automated feature. Greg Von Kuster !-- Locations of all bismark converted bs-seq references -- table name=bismark_bs_indeces comment_char=# columnsvalue, dbkey, name, path/columns file path=tool-data/bismark_bs_indeces.loc / /table On Nov 29, 2012, at 4:41 AM, Sachit Adhikari wrote: Hi all, I am seeing this error while clicking on Bismark in Galaxy. I got the Bismark for galaxy tool shed. I tried to get another bismark wrapper developed by Bjoern. I didnt know how to download that. What's the error? Thanks ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Downgrading toolshed tools
Hi Paul, From your explanation, it seems that you have 2 versions of the tool installed in your Galaxy instance, the original version and the new version that is broken. If this is the case, just uninstall the newer broken version, and continue to make only the previous working version available to your users. Rolling back an installed tool shed repository within a Galaxy installation has never been supported - instead just uninstall. Greg Von Kuster On Nov 14, 2012, at 11:06 AM, Paul-Michael Agapow wrote: Just today, we had a case where we wanted to rollback to a previous version of a tool that we'd installed from a toolshed. (No big reason except that our latest fix actually broke the tool.) Is there a way to do this? I could have sworn there was but couldn't find it in the admin interface. -- Paul Agapow (p...@agapow.net) ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Errors during database migration after updating galaxy
Hello Joel,
The main Galaxy tool shed is back up - thanks for reporting this problem.
Greg Von Kuster
On Sep 30, 2012, at 5:34 PM, Joel Rosenberg wrote:
It looks like the galaxy toolshed is down.
The migration script is trying to download this:
http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bwa_wrappersowner=devteamchangeset_revision=ffa8aaa14f7cwebapp=install_manager
But this:
http://toolshed.g2.bx.psu.edu
is down:
502 Bad Gateway
nginx/1.1.4
quote author='joel'
My cloud galaxy cluster can't boot up after attempting a bitbucket update
due to a 502 HTTP error when trying to update the DB. Here's the log:
From: thisisj...@hotmail.com
To: galaxy-user@lists.bx.psu.edu
Subject: Errors during database migration after updating galaxy
Date: Sun, 30 Sep 2012 21:18:11 +
My cloud galaxy cluster can't boot up after attempting a bitbucket update due
to a 502 HTTP error when trying to update the DB. Here's the log:
/mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
RuntimeWarning: __builtin__.file size changed, may indicate binary
incompatibility
from csamtools import *
python path is:
/mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/Fabric-1.4.2-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/ssh-1.7.14-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Paste-1.6-py2.6.egg,
/mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/,
/usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk,
/usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload
galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,317 Loading
references to tool sheds from tool_sheds_conf.xml
galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,317 Loaded
reference to tool shed: Galaxy main tool shed
galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,318 Loaded
reference to tool shed: Galaxy test tool shed
galaxy.model.migrate.check DEBUG 2012-09-30 21:13:18,344 psycopg2 egg
successfully loaded for postgres dialect
galaxy.model.migrate.check INFO 2012-09-30 21:13:18,610 At database version
107
galaxy.tool_shed.migrate.check DEBUG 2012-09-30 21:13:18,620 psycopg2 egg
successfully loaded for postgres dialect
Traceback (most recent call last):
File
/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py, line
36, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /mnt/galaxyTools/galaxy-central/lib/galaxy/app.py, line 47, in
__init__
verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
File
/mnt/galaxyTools/galaxy-central/lib/galaxy/tool_shed/migrate/check.py, line
54, in verify_tools
missing_tool_configs_dict = check_for_missing_tools( app,
tool_panel_configs, latest_tool_migration_script_number )
File
/mnt/galaxyTools/galaxy-central/lib/galaxy/tool_shed/migrate/common.py,
line 33, in check_for_missing_tools
response = urllib2.urlopen( url )
File /usr/lib/python2.6/urllib2.py, line 126, in urlopen
return _opener.open(url, data, timeout)
File /usr
Re: [galaxy-user] tool_path
Hello Fabien,
I don't understand the issue - can you provide a sample tool config that
includes these hard-coded paths? This initially sounds like an issue with the
tool configs, not the tool shed, but I may see the problem with your
clarification.
Thanks,
Greg Von Kuster
On Jul 3, 2012, at 9:58 AM, Fabien Mareuil wrote:
Hi,
I have read the exchange betwen you and Florent Angly about Problem with
new tool shed and I have a problem with Nebula Tools:
http://nebula.curie.fr/.
At the Pasteur Institute, we have 4 galaxy instances and I would like to
use a local tool shed instance for Nebula installation.
However, the nebula has tools with hard-coded path tool but I don't want
hard-coded this so do you have a solution to add a thing like this
${tool.install_dir} in the xml?
Thank you for your answer.
Best Regards,
Fabien Mareuil
___
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Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists,
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___
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Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
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Re: [galaxy-user] tool_path
Hello Fabien,
This issue is indeed due to the tool design and is not related to the tool
shed. I'm not primarily a tool developer, so I'm not the best person to help
you with this issue.
However, one recommendation would be to place your scripts and binaries that a
specific tool wrapper uses in the same directory as the tool wrapper so that
paths are not necessary. Some of the binaries may be more appropriately added
to the environment path used by the user that starts up your Galaxy instance (
the R binaries are a good example ). This is the approach that the tools
included in the Galaxy distribution use.
The tool shed will not do anything special with tool wrapper that include
hard-coded paths like this. The tool shed generally only makes sure that the
tool loads properly in Galaxy. However, recent enhancements to the tool shed
will handle tool dependencies that are properly defined in the tool config file
within the requirements tag set. These new tool shed features will soon be
documented in the tool shed wiki.
Thanks,
Greg Von Kuster
On Jul 3, 2012, at 12:27 PM, Fabien Mareuil wrote:
Hi,
Thank for your answer, I copy you a part of the shell code
LOCAL_DIR= #{GALAXY_DIR}/galaxy-dist/tools/AnnotateGenes
R_DIR= #{R_PATH}/bin
echo ChIP: $LOG
if [ -r $REG ]; then
echo 1: perl $LOCAL_DIR/geneAnnotation.pl -g
$LOCAL_DIR/$GENOME.noIdenticalTransc.txt -tf $CHIPFILE -selG $REG -o
$OUTSTAT -lp $LEFTPROM -rightp $RIGHTPROM -enh $ENH -dg $DOWNGENE
$LOGTMP
and a part of the xml
tool id=annotateGenes name=Annotation of genes with Chip-Seq peaks
version=1.0
description /description
command interpreter=bash #if $use_reg.use_reg_selector == no and
$use_control.use_control_selector == no #annotateGenes_wrapper.sh -f
$inputfile -y $log -l $left -o $outputPNG -r $right -d $DownGene -h
$EnhLeft -u $stats -v $input_organism.version #elif
$use_reg.use_reg_selector == no and $use_control.use_control_selector
== yes # annotateGene_wrapper.sh -f $inputfile -y $log -c $controlfile
-x $statsControl -o $outputPNG -l $left -r $right -d $DownGene -h
$EnhLeft -u $stats -v $input_organism.version #elif
$use_reg.use_reg_selector == yes and $use_control.use_control_selector
== no # annotateGenes_wrapper.sh -y $log -f $inputfile -e $regfile -l
$left -o $outputPNG -r $right -d $DownGene -h $EnhLeft -u $stats -v
$input_organism.version #else # annotateGenes_wrapper.sh -f $inputfile
-c $controlfile -x $statsControl -l $left -y $log -o $outputPNG -r $right
-d $DownGene -h $EnhLeft -u $stats -v $input_organism.version -e $regfile
#end if
This tools are avaible in : http://nebula.curie.fr/
You can see that the variable LOCAL_DIR is the PATH of the tool so I would
like to know if it's possible to obtain this information without
hard-coded this?
Thank you for your answer.
Best Regards,
Fabien Mareuil
Hello Fabien,
I don't understand the issue - can you provide a sample tool config that
includes these hard-coded paths? This initially sounds like an issue
with
the tool configs, not the tool shed, but I may see the problem with your
clarification.
Thanks,
Greg Von Kuster
On Jul 3, 2012, at 9:58 AM, Fabien Mareuil wrote:
Hi,
I have read the exchange betwen you and Florent Angly about Problem with
new tool shed and I have a problem with Nebula Tools:
http://nebula.curie.fr/.
At the Pasteur Institute, we have 4 galaxy instances and I would like
to
use a local tool shed instance for Nebula installation.
However, the nebula has tools with hard-coded path tool but I don't
want
hard-coded this so do you have a solution to add a thing like this
${tool.install_dir} in the xml?
Thank you for your answer.
Best Regards,
Fabien Mareuil
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
Re: [galaxy-user] Data upload...
Hi Greg, Upload your files to a Galaxy data library using a combination of Upload files from filesystem paths without copying data into Galaxy's default data store. See the following wiki for all the details: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files For all of the details about data libraries, see: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries Greg Von Kuster On Apr 23, 2012, at 11:26 AM, Gregory Miles wrote: We have large files that cannot be uploaded using the file upload command and instead would need to be uploaded using a URL. Unfortunately, we are using a local install on a non-local machine, so setting up an FTP server on this machine is a security issue. The files are located on this computer already anyhow, and Galaxy would simply be copying from one folder to another in order to perform the get data step. Is there a simple way to have a pointer of some sort such that galaxy knows where this file is and: 1) Would not have to copy it and could simply refer to the file location. 2) Could perform data analysis steps on this file and push the output to the usual location (not the location of the data files). Any help would be greatly appreciated. Thanks. Dr. Gregory Miles Bioinformatics Specialist Cancer Institute of New Jersey @ UMDNJ Office: (732) 235 8817 - CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Data upload...
Hi Greg, Even though you are not copying the data into Galaxy's default data store, Galaxy determines and stores certain metadata for each of the data files to which you are linking. One of the types of metadata defined for the Bam datatypes is it's index, which is created by a call to samtools. Unfortunately there is really no way around this because Galaxy requires the index file to be in a correct state, and I believe the test to determine correctness is at least as intensive as generating the index in the first place. It's been a while since I was involved in this (specifically setting metadata for bam files using samtools), so perhaps samtools has been recently improved in this regard. if so, I'll look to others to let me know I'm now outdated in my understanding of this. If we need to update samtools used by the Galaxy code to take advantage of newer features, we can certainly do so. Greg Von Kuster On Apr 23, 2012, at 2:51 PM, Gregory Miles wrote: Thank you very much for your help with this - we got that settled. One other question...we are importing sorted, indexed bam files into a galaxy data library and we are not having galaxy copy over the files (they are large) but rather just setting up galaxy such that it points to the relevant directory. We noticed that the file (160 GB in size) is taking a long time to import considering all it should be doing is creating a link. When we examined processes that are running, we noticed that samtools is running. From searching around a bit, it seems that Galaxy does this in order to groom the bam file (sort/index) and ensure that it is in the format necessary for galaxy to be able to interpret it. Is there any way around this? We did the sorting and indexing prior to import and it's taking quite a while to perform an unnecessary function. Thanks. Greg Dr. Gregory Miles Bioinformatics Specialist Cancer Institute of New Jersey @ UMDNJ Office: (732) 235 8817 - CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. On Mon, Apr 23, 2012 at 12:55 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Greg, Upload your files to a Galaxy data library using a combination of Upload files from filesystem paths without copying data into Galaxy's default data store. See the following wiki for all the details: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files For all of the details about data libraries, see: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries Greg Von Kuster On Apr 23, 2012, at 11:26 AM, Gregory Miles wrote: We have large files that cannot be uploaded using the file upload command and instead would need to be uploaded using a URL. Unfortunately, we are using a local install on a non-local machine, so setting up an FTP server on this machine is a security issue. The files are located on this computer already anyhow, and Galaxy would simply be copying from one folder to another in order to perform the get data step. Is there a simple way to have a pointer of some sort such that galaxy knows where this file is and: 1) Would not have to copy it and could simply refer to the file location. 2) Could perform data analysis steps on this file and push the output to the usual location (not the location of the data files). Any help would be greatly appreciated. Thanks. Dr. Gregory Miles Bioinformatics Specialist Cancer Institute of New Jersey @ UMDNJ Office: (732) 235 8817 - CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information
Re: [galaxy-user] Data upload...
Is there something helpful in your paster log about the cause? On Apr 23, 2012, at 4:34 PM, Gregory Miles wrote: Thanks again for the feedback...one final (hopefully) thingas I mentioned in first e-mail, we are trying to add a large (~170 GB) BAM file to a library with just a link to the file (no copying). After at least an hour of working, I get the error message Unable to finish job, tool error. Any thoughts as to how I can fix this? Thanks. Greg On 4/23/12, Greg Von Kuster g...@bx.psu.edu wrote: Hi Greg, Even though you are not copying the data into Galaxy's default data store, Galaxy determines and stores certain metadata for each of the data files to which you are linking. One of the types of metadata defined for the Bam datatypes is it's index, which is created by a call to samtools. Unfortunately there is really no way around this because Galaxy requires the index file to be in a correct state, and I believe the test to determine correctness is at least as intensive as generating the index in the first place. It's been a while since I was involved in this (specifically setting metadata for bam files using samtools), so perhaps samtools has been recently improved in this regard. if so, I'll look to others to let me know I'm now outdated in my understanding of this. If we need to update samtools used by the Galaxy code to take advantage of newer features, we can certainly do so. Greg Von Kuster On Apr 23, 2012, at 2:51 PM, Gregory Miles wrote: Thank you very much for your help with this - we got that settled. One other question...we are importing sorted, indexed bam files into a galaxy data library and we are not having galaxy copy over the files (they are large) but rather just setting up galaxy such that it points to the relevant directory. We noticed that the file (160 GB in size) is taking a long time to import considering all it should be doing is creating a link. When we examined processes that are running, we noticed that samtools is running. From searching around a bit, it seems that Galaxy does this in order to groom the bam file (sort/index) and ensure that it is in the format necessary for galaxy to be able to interpret it. Is there any way around this? We did the sorting and indexing prior to import and it's taking quite a while to perform an unnecessary function. Thanks. Greg Dr. Gregory Miles Bioinformatics Specialist Cancer Institute of New Jersey @ UMDNJ Office: (732) 235 8817 - CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. On Mon, Apr 23, 2012 at 12:55 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Greg, Upload your files to a Galaxy data library using a combination of Upload files from filesystem paths without copying data into Galaxy's default data store. See the following wiki for all the details: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files For all of the details about data libraries, see: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries Greg Von Kuster On Apr 23, 2012, at 11:26 AM, Gregory Miles wrote: We have large files that cannot be uploaded using the file upload command and instead would need to be uploaded using a URL. Unfortunately, we are using a local install on a non-local machine, so setting up an FTP server on this machine is a security issue. The files are located on this computer already anyhow, and Galaxy would simply be copying from one folder to another in order to perform the get data step. Is there a simple way to have a pointer of some sort such that galaxy knows where this file is and: 1) Would not have to copy it and could simply refer to the file location. 2) Could perform data analysis steps on this file and push the output to the usual location (not the location of the data files). Any help would be greatly appreciated. Thanks. Dr. Gregory Miles Bioinformatics Specialist Cancer Institute of New Jersey @ UMDNJ Office: (732) 235 8817 - CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use
Re: [galaxy-user] Toolshed initial upload errors out
Hi Paul, On Apr 10, 2012, at 9:15 AM, Paul-Michael Agapow wrote: As per the title, I’m trying to setup a toolshed for our local use. After creating a repo, I try to upload the initial file only to get: TypeError: array item must be char Which seems to happen repeatedly, i.e. it’s not a passing error. I'll need to see your paster log to be able to help on this one. You can view it using tail -f community_webapp.log (without the quotes) from your Galaxy install directory. Can you respond back with the content? While I’m here, a perhaps obvious question: where or how does the main Galaxy instance get the list of toolsheds to display? The main and test sheds are hardcoded in, I guess, but how does it pick up the local – simply by virtue of the fact that it is local? The list of tool sheds available to any local Galaxy instance is defined in the tool_sheds_conf.xml file in the Galaxy install directory. For your local shed, you'll simply need to an entry like this: tool_shed name=Bx tool shed url=http://gvk.bx.psu.edu:9009// p Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Health Protection Agency Thanks, Greg Von Kuster ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Blast2GO local instance Re: Table with gene count reads
On Apr 3, 2012, at 6:07 AM, Peter Cock wrote: On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster g...@bx.psu.edu wrote: On Mar 24, 2012, at 7:30 AM, Peter Cock wrote: Have you seen the README file that comes with the Blast2GO wrapper? Perhaps the 'install from toolshed' could be tweaked to make this kind of documentation more visible... If you are installing a single repository that contains a file named one of (case is ignored) readme, readme.txt, read_me, read_me.txt, the contents of the file will be displayed on the tool panel section selection page. An example using the antismash repository on the main tool shed is below. This new feature is available in change set revision 6945:5ea04ccb61e8, which is currently running on the Galaxy tool shed and our central development repository. It will be available in the next Galaxy distribution. Great. In this case I've actually called the file blast2go.txt (to match the use of blast2go.xml and blast2go.py). I didn't want to use a generic name like README since there could be other tools installed in the same folder (this predates the auto-install system). Is this naming pattern common used enough to justify including in the Galaxy Tool Shed code for spotting a README file? Since the read me file contains instructions for installing the tools in the repository, would it be better to assume only 1 installation file that includes different instructions per contained tool if necessary? If multiple read me files are allowed per repository, they would all have to be merged together with the entire content displayed on the tool panel section selection screen anyway, so allowing only a single file would be better. The read me in your blast2go repository is named blast2go.txt, so I suppose we could expand the read me file name list to include repository name.txt. I'll do this. Care must be taken when following instructions in README files since some of the information may be outdated. For example, the Galaxy functional test framework was recently enhanced to support testing tools included in installed repositories, but I've seen some README files currently in repositories that instruct installers to move test data to the Galaxy installation environment, which is no longer necessary. Some of my tools' README files will need a little clarification following those changes to Galaxy. My next big feature will be supporting installation of tool dependencies automatically with the repository contents, so keep that in mind if you're making changes to install instructions. This enhancement will take a bit of time. Thanks, Peter ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Incorrect permissions when uploading files
Hi Jim, This behavior is likely due to permissions that are combined / derived / inherited to the location of the data library at which you are uploading, although it is not possible to be definite without more information about the permissions you have set at the library, folder, etc. Galaxy will ensure that the dataset is accessible to at least 1 user, so association access to a private role and then attempting to provide more open access with a public / group role at a lower level in the library hierarchy could be problematic. Check our Data Library security wiki if you haven't seen it yet - http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Library%20Security. Hopefully it will clarify why you're seeing this. If not, you'll have to let me know the permissions at all levels of your library in order for me to be able to help. Thanks, Greg Von Kuster On Mar 10, 2012, at 1:15 PM, James Vincent wrote: Hello, I think there is a problem with the way permissions are set when uploading files. As admin, when I add new files to a library by file path upload, I select just one specific role which is a group of people (at the bottom of the upload page). There are several different roles available, as well as single users. When I select the single role, it gets highlighted as expected in the drop down list and I click Upload to library. After upload is complete I find that the Access permissions always include me as a single user in addition to the role I actually selected during upload. This causes access to be denied to the role (the group) because there is now a personal role associated with the library. Is this a bug? How can I really get just a single role associated to Access permissions on upload? Thanks, Jim ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!!
Do you restart your Galaxy server when you make changes to universe_wsgi.ini (like adding / uncommenting email addresses for the admin_users setting)? On Mar 1, 2012, at 12:56 PM, Alejandra Rougon wrote: Thanks Jennifer, I already uncomment and add my email address but still the admin link does not appear. I then registered my email in users and logged in with that email address and I still don't see the link. when I type /admin at the of the url it says that I have to be logged in as an administrator. sorry I am a newbe on this admin stuff. From: Jennifer Jackson j...@bx.psu.edu To: Alejandra Rougon alerou...@yahoo.com Cc: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu; closetic...@galaxyproject.org closetic...@galaxyproject.org Sent: Tuesday, 28 February 2012, 17:19 Subject: Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! Hi, You will want to assign yourself as an administrator in the universe_wsgi.ini file. # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: # http://wiki.g2.bx.psu.edu/Admin/Interface #admin_users = None ^^ uncomment and add your login email here Other wikis that may be helpful, especially if user login is not yet set up: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server http://wiki.g2.bx.psu.edu/Admin/Config Hopefully this helps, Jen Galaxy team On 2/28/12 2:59 PM, Alejandra Rougon wrote: Thank you Greg, I saw the wiki but I do not see the admin link in my galaxy interface. How do you open galaxy as an administrator? t *From:* Greg Von Kuster g...@bx.psu.edu *To:* Alejandra Rougon alerou...@yahoo.com *Cc:* galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu *Sent:* Tuesday, 28 February 2012, 14:02 *Subject:* Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! You can upload your large file to Galaxy data libraries using a combination of Upload files from filesystem paths and Do not copy data into Galaxy's default file store. See this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files For all of the information on Galaxy data libraries, see this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries Greg Von Kuster On Feb 28, 2012, at 2:54 PM, Alejandra Rougon wrote: Hello, I tried to search in the forums and although this question has appeared many times I still don't have a solution. I cannot manage to upload big files into the local galaxy, it just takes ages. Can I not just copy and paste into a local directory? why do I have to upload the files if it is already installed locally? I do not have a server webpage in order to use the url address option If I do it through ftp (locally) what ftp address shall I put? ftp localhost:8080?? Is there any other option to speed up uploading, is so slow that is no longer worth using it, please help me! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your
Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!!
No, you'll need to stop and restart your Galaxy server. On Mar 1, 2012, at 2:01 PM, Alejandra Rougon wrote: I did close the web browser and opened it again was that enough? From: Greg Von Kuster g...@bx.psu.edu To: Alejandra Rougon alerou...@yahoo.com Cc: Jennifer Jackson j...@bx.psu.edu; galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu; closetic...@galaxyproject.org closetic...@galaxyproject.org Sent: Thursday, 1 March 2012, 12:46 Subject: Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! Do you restart your Galaxy server when you make changes to universe_wsgi.ini (like adding / uncommenting email addresses for the admin_users setting)? On Mar 1, 2012, at 12:56 PM, Alejandra Rougon wrote: Thanks Jennifer, I already uncomment and add my email address but still the admin link does not appear. I then registered my email in users and logged in with that email address and I still don't see the link. when I type /admin at the of the url it says that I have to be logged in as an administrator. sorry I am a newbe on this admin stuff. From: Jennifer Jackson j...@bx.psu.edu To: Alejandra Rougon alerou...@yahoo.com Cc: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu; closetic...@galaxyproject.org closetic...@galaxyproject.org Sent: Tuesday, 28 February 2012, 17:19 Subject: Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! Hi, You will want to assign yourself as an administrator in the universe_wsgi.ini file. # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: # http://wiki.g2.bx.psu.edu/Admin/Interface #admin_users = None ^^ uncomment and add your login email here Other wikis that may be helpful, especially if user login is not yet set up: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server http://wiki.g2.bx.psu.edu/Admin/Config Hopefully this helps, Jen Galaxy team On 2/28/12 2:59 PM, Alejandra Rougon wrote: Thank you Greg, I saw the wiki but I do not see the admin link in my galaxy interface. How do you open galaxy as an administrator? t *From:* Greg Von Kuster g...@bx.psu.edu *To:* Alejandra Rougon alerou...@yahoo.com *Cc:* galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu *Sent:* Tuesday, 28 February 2012, 14:02 *Subject:* Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!! You can upload your large file to Galaxy data libraries using a combination of Upload files from filesystem paths and Do not copy data into Galaxy's default file store. See this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files For all of the information on Galaxy data libraries, see this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries Greg Von Kuster On Feb 28, 2012, at 2:54 PM, Alejandra Rougon wrote: Hello, I tried to search in the forums and although this question has appeared many times I still don't have a solution. I cannot manage to upload big files into the local galaxy, it just takes ages. Can I not just copy and paste into a local directory? why do I have to upload the files if it is already installed locally? I do not have a server webpage in order to use the url address option If I do it through ftp (locally) what ftp address shall I put? ftp localhost:8080?? Is there any other option to speed up uploading, is so slow that is no longer worth using it, please help me! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http
Re: [galaxy-user] Speed up uploading into local Galaxy, terribly slow!!
You can upload your large file to Galaxy data libraries using a combination of Upload files from filesystem paths and Do not copy data into Galaxy's default file store. See this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files For all of the information on Galaxy data libraries, see this wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries Greg Von Kuster On Feb 28, 2012, at 2:54 PM, Alejandra Rougon wrote: Hello, I tried to search in the forums and although this question has appeared many times I still don't have a solution. I cannot manage to upload big files into the local galaxy, it just takes ages. Can I not just copy and paste into a local directory? why do I have to upload the files if it is already installed locally? I do not have a server webpage in order to use the url address option If I do it through ftp (locally) what ftp address shall I put? ftp localhost:8080?? Is there any other option to speed up uploading, is so slow that is no longer worth using it, please help me! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] upgrade script
Hello Victor,
The following statement in your log is concerning because it looks like
something in your environment got corrupted in some way.
Exception: Your database has version '90' but this code expects version '79'.
Clean database schema migration upgrades go from smaller to larger numbers
(e.g., 89 - 90, 90 - 91, etc). Your migrate_versions.version database table
column has a value of 90, but your ~/lib/galaxy/model/migrate/versions
sub-directory has scripts only up to 0079... (or so it seems). Not sure how
best to fix the problem...
Greg Von Kuster
On Feb 21, 2012, at 2:21 PM, Victor Ruotti wrote:
Hi,
I'm trying to use the upgrade script given that the current schema is now
version 90.
I get the following error.
Can anyone point me out, maybe there is something to do before upgrading?
thanks in advance.
Victor
trying to start galaxy I get
Traceback (most recent call last):
File /opt/galaxy/galaxy-dist-original/lib/galaxy/web/buildapp.py, line 82,
in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /opt/galaxy/galaxy-dist-original/lib/galaxy/app.py, line 32, in
__init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
File /opt/galaxy/galaxy-dist-original/lib/galaxy/model/migrate/check.py,
line 105, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '90' but this code expects version '79'.
Please backup your database and then migrate the schema by running 'sh
manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
Removing PID file runner0.pid
--trying to upgrade
sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade
Traceback (most recent call last):
File ./scripts/manage_db.py, line 63, in module
main( repository=repo, url=db_url )
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py,
line 150, in main
ret = command_func(**kwargs)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py,
line 327, in _migrate
changeset = schema.changeset(version)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py,
line 173, in changeset
changeset = self.repository.changeset(database, start_ver, version)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py,
line 170, in changeset
changes = [self.version(v).script(database, op) for v in versions]
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py,
line 145, in version
return self.versions.version(*p, **k)
File
/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/version.py,
line 125, in version
return self.versions[VerNum(vernum)]
KeyError: VerNum(90)
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Galaxy analysis and other features on the public server
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local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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Galaxy analysis and other features on the public server
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To manage your subscriptions to this and other Galaxy lists,
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Re: [galaxy-user] Production environment
David, I can answer your first question, but will leave it to others to answer your second as I am less likely to answer it correctly. Regarding uploading files from your server, use the Upload files (to data libraries) from file system paths but do not copy into Galaxy's default file store. For details about the various upload options to Galaxy data libraries, see http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files. For complete details about Galaxy data libraries, see http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries. Greg On Feb 10, 2012, at 3:28 AM, David Castillo wrote: Hello, I've just installed Galaxy in my server in order to run it locally but there's a couple of tasks I haven't been able to complete, I hope somebody could advice me on how to accomplish them: I wanted to be able to have direct access to the contents stored in my server, so when click on 'Get Data'; 'Upload File' I can get the files stored in my server instead of the files stored in my personal computer. Is this even possible? If not, what other options do I have if I want to load heavy packages (~3 GB) without having to wait much? I haven't been able to 'Edit' Workflows like in the public server, I have been able to create them, but once I try to edit them it just attempts to load the 'Workflow Editor' but it never does. How can I solve this? Do I have to configure something before attempting to do this? Thanks in advance, David ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Velvetoptimiser error
Hello Efthymios,In case no one on this list answers, you may be able to get an answer to your question by contacting the owner of the velvetoptimiser repository. You can do this by selecting the "Contact repository owner" menu item on the View repository page.On Dec 20, 2011, at 4:02 AM, Makis Ladoukakis wrote:Dear Galaxy users,Has anyone worked with velvetoptimiser tool from the Tool shed?I have been trying both the stable and the test version of the velvetoptimiser tool and i keep getting the same error:Traceback (most recent call last): File "/home/ladoukef/galaxy_dist/tools/myTools/velvetoptimiser/velvet_optimiser.py", line 102, in if __name__ == "__main__": __main__() File "/home/ladoukef/galaxy_dist/tools/myTools/velvetoptimiser/velvet_optimiser.py", line 67, in __main__ for line in open(contigs_path ):IOError: [Errno 2] No such file or directory: 'contigs.fa'Can someone identify where the error is? The file missing (contigs.fa) is supposed to be built by the tool itself.Thank you,Efthymios Ladoukakis___The Galaxy User list should be used for the discussion ofGalaxy analysis and other features on the public serveratusegalaxy.org. Please keep all replies on the list byusing "reply all" in your mail client. For discussion oflocal Galaxy instances and the Galaxy source code, pleaseuse the Galaxy Development list:http://lists.bx.psu.edu/listinfo/galaxy-devTo manage your subscriptions to this and other Galaxy lists,please use the interface at:http://lists.bx.psu.edu/ Greg Von KusterGalaxy Development Teamg...@bx.psu.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] How to determine version of Galaxy from main page
Hello Greg, Galaxy does not have versions as you'd find in commercial products. There is a strict requirement that Galaxy provide reproducible behavior always, so any new feature introduced into Galaxy (or any enhancement to an existing feature) must not break any older feature that came before. Because of this, you can always think of Galaxy as being version 1 if it helps. Galaxy does, however have different distributed builds or mercurial changeset revision numbers. You can find out what build your own local instance is running if you type hg heads in the Galaxy install directory of your local Galaxy instance. The build of the main public Galaxy instance is included in the following string on the main page in the center panel. Galaxy build: $Rev 6299:b258de1e6cea$ The various builds that are made available in the distribution are always documented in each of the associated news briefs that announce whats availabe in each new distribution. See our wiki at http://wiki.g2.bx.psu.edu/News%20Briefs. On Dec 21, 2011, at 4:24 PM, Greg Edwards wrote: Hi folks, I've researched this in the new global Google Search tool http://galaxy.psu.edu/search/web/ but didn't see the answer I needed. Is there actually a single version of Galaxy ? or is it a collection of components with their own versions ? Can that can be seen on or near the Main front page ? I can't see a Version/About type of item, either in menus or lurking in some rev stamp at the bottom of pages etc. Thanks. -- Greg Edwards gedwar...@gmail.com ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] [galaxy-dev] Importing existing data into Galaxy
Data libraries are accessible from the Shared Data pop-up menu in the top Galaxy menu bar. On Oct 28, 2011, at 1:12 PM, Oren Livne wrote: Dear Greg, Thanks so much, this helps a lot. I created a public data library, but it is not listed in the list of libraries on the left pane in Analyze Data. How can I access it and use its files in workflows? Oren On 10/27/2011 7:55 PM, Greg Von Kuster wrote: Oren, The best way to do this would be to use galaxy data libraries, uploading files from file system paths and not copying the files into the Galaxy file location. The following provides all of the details about data libraries: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries The following provides specific details about the various options for uploading files to data libraries. http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Let us know if you encounter any issues. Greg Von Kuster On Oct 27, 2011, at 4:31 PM, Oren Livne wrote: Dear All, We have a large collection of large data files on our shared file system. We would like to make a subset of them available to a galaxy user session (based on user privileges; different subsets for different users). We want to leave files in their original locations and point galaxy to their paths without copying them. What is the best option for implementing this bridge? Remote data source/data library uploaded on the fly/other? Thanks, Oren ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Permissions and private roles
Anthony, Yours may be a corner case scenario that isn't properly handled, although I'm not sure it's critical as the data you want protected is, in fact, protected (or am I still not seeing it correctly?). If you feel this is a bug, please submit a ticket, although this is far off my development plans for the forsee-able future. Thanks! On Oct 25, 2011, at 4:30 AM, Anthony Underwood wrote: HI Greg Sorry for the confusion. The links are to screenshot uploads of Galaxy showing the folder visibilities. If it’s still not clear please send a quick mail. Thanks Anthony On 24/10/2011 19:01, Greg Von Kuster g...@bx.psu.edu wrote: I'm not following you here - please decipher your folder names, which I assume are mapped to your encoded request strings. On Oct 24, 2011, at 1:27 PM, Anthony Underwood wrote: Re: [galaxy-user] Permissions and private roles Thanks for the reply Greg Still don’t think I’ve quite got it in my head though it’s becoming clearer. I have 2 users each whom I have given permission to access 2 datasets. user 1 has access to data in a folder called 1st result and user 2 has access to data found in both a folder called fastqs and 2nd result (very artificial data scenario:)) user 1 can see http://cl.ly/3M3t0P2n3H101P1z393e I would not have expected him to see the fastqs folder user 2 can see http://cl.ly/1r2y1h2c0F0a0V403F1f I would not have expected them to be able to see 1st result. Thanks for your patience Anthony ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Permissions and private roles
Hello Anthony, On Oct 24, 2011, at 10:01 AM, Anthony Underwood wrote: Hi Greg Thanks for the reply. I can see now that as an admin user I can now add private roles using the Admin View as opposed to the data libraries view. It is still a bit unclear how a folder can be visible to one user but not to another. If both users have access to the library then they can view all folders, correct? Permissions on a folder are derived from permissions on specific datasets contained in the folder. So, if folder1 contains dataset1 and dataset2, and only Jack can see dataset 1 in folder1 and only Jill can see dataset2 in Folder1, both Jack and Jill can see Folder1, but Spot cannot. In addition, even though both Jack and Jill can see Folder1, each of them will be able to see only their respective dataset. I can see how I can edit add/modify permissions for a folder but not the view/access permission. Also another question about permissions. If I create a Galaxy page and share that with limited users then it appears that the datasets are all public via a URL is that correct? I'm not the expert on pages, Jeremy, can you answer this one? Thanks again Anthony On 24/10/2011 14:09, Greg Von Kuster g...@bx.psu.edu wrote: Hello Anthony, On Oct 24, 2011, at 6:55 AM, Anthony Underwood wrote: Permissions and private roles Hi all I’m trying to get my head round permissions on Data Libraries. I have a couple of questions 1) When I come to give access to a library the only roles I see are the current (admin) user’s private roles and other non-private roles I have created - no other private roles. The list of roles you see on the permission page for data library items ( folders and datasets ) is dependent upon the following: 1. Whether you are setting permissions on the library item from the Admin view ( where you should see both private and public roles ) or the Data Libraries view ( where you should only see your own private roles along with certain other public roles 2. The level in the hierarchy of the data library at which you are setting permissions. At the top level ( the data library level ), you have the ability to set the LIBRARY_ACCESS permission for the entire data library hierarchy. Depending upon the roles you associate here, all lower levels in the data library hierarchy show only those roles that are derived from the roles you set at the top LIBRARY_ACCESS permission. This is because it makes no sense to allow user john to have some permission to do something in a lower folder of a data library when he is not associated with the permission to even access the library at the top level. Reading the wiki page suggests that I should see all roles private and non-private. Not knowing which wiki you've read, make sure to see these: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Library%20Security http://wiki.g2.bx.psu.edu/Events/GDC2010?action=AttachFiledo=gettarget=GDC2010_data_libraries_sample_tracking.pdf 2) Is there a way to give a role access to just one folder of a library rather than the whole library? Yes, but again, the user with the role must be able to access the data library ( either the data library is public, or the user with the role is associated with the LIBRARY_ACCESS permission at the top level. Many thanks Anthony Dr Anthony Underwood Bioinformatics Group | Applied Laboratory and Bio- Informatics Unit Microbiology Services, Colindale Health Protection Agency ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://usegalaxy.org . Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu
Re: [galaxy-user] Permissions and private roles
I'm not following you here - please decipher your folder names, which I assume are mapped to your encoded request strings. On Oct 24, 2011, at 1:27 PM, Anthony Underwood wrote: Thanks for the reply Greg Still don’t think I’ve quite got it in my head though it’s becoming clearer. I have 2 users each whom I have given permission to access 2 datasets. user 1 has access to data in a folder called 1st result and user 2 has access to data found in both a folder called fastqs and 2nd result (very artificial data scenario:)) user 1 can see http://cl.ly/3M3t0P2n3H101P1z393e I would not have expected him to see the fastqs folder user 2 can see http://cl.ly/1r2y1h2c0F0a0V403F1f I would not have expected them to be able to see 1st result. Thanks for your patience Anthony ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Problem with new tool shed
Hello Forent, On Oct 13, 2011, at 2:48 AM, Florent Angly wrote: But maybe I need a little bit of guidance with this because the example shown, the user is given a _limited_ number of output datasets to choose from. The Grinder case seems simple: give the user a field where he can specify the number of output he wants, say, 2, 10, or 100 and produce as many datasets as needed. So, in the output section, the only reasonable way to process the output would be to have some sort of loop. Is this possible? This is not yet possible. This is something that has been desired for some time, but is not on our near-future plans for implementation. Thank you, Florent Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Problem with new tool shed
Hello Florent,
Thanks for your comments and suggestions - see my inline comments.
On Oct 4, 2011, at 11:42 PM, Florent Angly wrote:
Hi Greg,
I have a few additional comments and questions though:
1/ In the universe_wsgi.ini file, maybe the tool_config_file parameter could
be renamed to tool_config_files (plural) to indicate that it takes a list of
files.
I considered this, but held off on making this change since it would require
all local Galaxy installations to change as well. I'll soon enhance the
setting to behave the same way for both terms (tool_config_file or
tool_config_files) , so backward compatibility will not be a problem and using
the plural term will be more clear. Thanks for the suggestion.
2/ It seems like the Tools Search box cannot find newly installed tools.
However, after I restart Galaxy, it works as intended again.
I haven't got the search hooked up to the installed tools yet, but will very
soon. Thanks for finding and reporting this issue.
3/ In the Grinder wrapper, I relied on installing the wrapper under a
specific folder: ./tools/ngs simulation/grinder. The new wrapper installation
procedure installs the tools in the ../shed_tools/ folder and the admins can
choose under what category the tool is to be placed. This means that my
Grinder wrapper fails since it does not know where to find the scripts it
needs. Is there a way to get the directory where a tool is installed? Here is
an excerpt of the Grinder wrapper so you can better understand what I am
trying to do. This wrapper first runs Grinder and then moves its files (the
number of files is hard to determine ahead of time) to a place where Galaxy
will find them (see the wiki page
http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files under section
Number of Output datasets cannot be determined until tool run).
I've looked at your tool, and I think it would be beneficial if I provided
something like ${tool.install_dir}. This feature would allow you to eliminate
the use of hard-coded paths in your tools like the following which can
generally be counted on to break at some point. I should have this feature
available fairly soon ( I'm out of the lab this week, but will be back next
week ). Your tool should then be enhanced to use this new feature - I'll let
you know when it's available.
#set $tool_dir = os.path.join( os.path.abspath($__root_dir__), 'tools',
'ngs_simulation' )
Thanks,
Florent
command
#set $tool_dir = os.path.join( os.path.abspath($__root_dir__), 'tools',
'ngs_simulation' )
#set $script1 = os.path.join( $tool_dir, 'stderr_wrapper.py' )
#set $script2 = os.path.join( $tool_dir, 'grinder_multiple_outputs.py' )
$script1
grinder
#if $reference_file.specify == builtin:
-reference_file ${ filter( lambda x: str( x[0] ) == str(
$reference_file.value ), $__app__.tool_data_tables[ 'all_fasta'
].get_fields() )[0][-1] }
#else if $reference_file.specify == uploaded:
-reference_file $reference_file.value
#end if
[...]
#if str($homopolymer_dist):
-homopolymer_dist $homopolymer_dist
#end if
#set $output_dir = $__new_file_path__
-output_dir $output_dir
#set $base_name = $output.id
-base_name $base_name
;
$script2 $output_dir $base_name
/command
On 04/10/11 22:55, Greg Von Kuster wrote:
Hello Florent,
Sorry for the confusion on this - we are preparing a new Galaxy
distribution, and the tool shed wiki has been written in preparation for it.
The new distribution will be available fairly soon, and the Galaxy News
Brief will include information about these new tool shed features. In any
case, you have already discovered that you can use in if you update your
Galaxy instance to the latest Galaxy development repository ( Galaxy central
).
The problem you see is most likely caused by your not having configured an
additional tool_config_file setting in your universe_wsgi.ini. Look for
something like following in your latest version of the
universe_wsgi.ini.sample that you got when you updated from Galaxy central.
# Locally installed tools and tools installed from tool sheds
tool_config_file = tool_conf.xml,shed_tool_conf.xml
If you add a new additional file name like shed_tool_conf.xml, you should
not have a problem installing from a tool shed. I'll have a fix for the bug
you've discovered shortly, but making this change will fix the behavior
until then.
Let me know if you bump into any additional problems.
Thanks for finding this!
Greg Von Kuster
On Oct 4, 2011, at 2:53 AM, Florent Angly wrote:
Hi all,
I tried the latest stable version of Galaxy:
http://wiki.g2.bx.psu.edu/News%20Briefs/2011_08_30. This page has links to
how to use the new tool shed including how to automatically deploy tools
from the shed in a local Galaxy server
Re: [galaxy-user] How to delete multiple items in libraries?
Hello Louise-Amelie, This behavior was corrected in change set 5612:3297ec86d657, which should be available in the distribution within the next week or so. Sorry for the inconvenience. Greg Von Kuster On Jun 20, 2011, at 11:06 AM, Louise-Amélie Schmitt wrote: Hello everyone In the admin panel Manage data libraries section I have an issue with deleting datasets. When I click on each dataset's triangle menu and ask for deletion, everything is fine. But whenever I select datasets and ask for deletion with the drop down menu at the bottom of the page, Galaxy tells me I don't have the rights to delete them. I get the following message: You are not authorized to delete any of the selected datasets. Did I miss anything? Thanks, L-A ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] biomart error
Hello Lisa, I noticed your stack trace in another message you sent - pasted below. If this is the problem you are seeing, then upgrading your Galaxy instance to the latest version will fix the problem. This issue was fixed in change set 5589. This is the exact error I am getting... Traceback (most recent call last): File galaxy_dist/lib/galaxy/jobs/runners/local.py, line 58, in run_job job_wrapper.prepare() File galaxy_dist/lib/galaxy/jobs/__init__.py, line 361, in prepare self.tool.exec_before_job( self.queue.app, inp_data, out_data, param_dict ) File galaxy_dist/lib/galaxy/tools/__init__.py, line 1881, in exec_before_job json_params[ 'param_dict' ] = self._prepare_datasource_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? File galaxy_dist/lib/galaxy/tools/__init__.py, line 1867, in _prepare_datasource_json_param_dict rval[ key ] = self._prepare_datasource_json_list( val ) NameError: global name 'val' is not defined Greg Von Kuster On May 31, 2011, at 11:06 AM, Liisa Koski wrote: I am also getting the same error with my local biomart and local galaxy installations. Thanks, Liisa From: Jennifer Jackson j...@bx.psu.edu To: Christophe Klopp christophe.kl...@toulouse.inra.fr Cc: galaxy-user@lists.bx.psu.edu Date: 2011-05-31 09:32 Subject: Re: [galaxy-user] biomart error Sent by: galaxy-user-boun...@lists.bx.psu.edu Hello Christophe, I am unable to duplicate - BioMart appears to be functioning as expected this morning. Would you have time to run your query again? If the problem persists, if you could share your history with me (Options - Share or Publish - email back link) and list out the exact steps that you are performing, that would be very helpful. Best, Jen Galaxy team On 5/30/11 8:33 AM, Christophe Klopp wrote: Hi, I've tried a simple query in biomart : retrieve all gene locations for the Danio rerio in Ensembl 62 and I get an error : An error occurred running this job: /failure preparing job / The same happens with the test site? Cheers Christophe/ / -- = Christophe KLOPP BIAINRA Toulouse 31326 Castanet-Tolosan = = Tel: 33 5 61 28 50 36 Email:christophe.kl...@toulouse.inra.fr = =http://www.sigenae.org/ = =http://bioinfo.genotoul.fr/ = ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http
Re: [galaxy-user] biomart error
Hi Lisa, Very sorry for the confusion - you are correct! The tip of the galaxy-dist repo at https://bitbucket.org/galaxy/galaxy-dist is change set 5585, so the fix is not available in the dist repo yet, and probably won't be there for another few weeks. If you don't want to wait, you can pull the fix from our development repo at https://bitbucket.org/galaxy/galaxy-central. Greg Von Kuster On May 31, 2011, at 11:52 AM, Liisa Koski wrote: Hi Greg, I thought I was up to date. When I run the following command I get 'no changes found' hg incoming real URL is https://bitbucket.org/galaxy/galaxy-dist comparing with http://www.bx.psu.edu/hg/galaxy searching for changes no changes found [galaxy@galaxy_dist]$ Thanks, Liisa From: Greg Von Kuster g...@bx.psu.edu To: Liisa Koski liisa.ko...@dnalandmarks.ca Cc: j...@bx.psu.edu, galaxy-user@lists.bx.psu.edu, galaxy-user-boun...@lists.bx.psu.edu Date: 2011-05-31 11:29 Subject: Re: [galaxy-user] biomart error Hello Lisa, I noticed your stack trace in another message you sent - pasted below. If this is the problem you are seeing, then upgrading your Galaxy instance to the latest version will fix the problem. This issue was fixed in change set 5589. This is the exact error I am getting... Traceback (most recent call last): File galaxy_dist/lib/galaxy/jobs/runners/local.py, line 58, in run_job job_wrapper.prepare() File galaxy_dist/lib/galaxy/jobs/__init__.py, line 361, in prepare self.tool.exec_before_job( self.queue.app, inp_data, out_data, param_dict ) File galaxy_dist/lib/galaxy/tools/__init__.py, line 1881, in exec_before_job json_params[ 'param_dict' ] = self._prepare_datasource_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? File galaxy_dist/lib/galaxy/tools/__init__.py, line 1867, in _prepare_datasource_json_param_dict rval[ key ] = self._prepare_datasource_json_list( val ) NameError: global name 'val' is not defined Greg Von Kuster On May 31, 2011, at 11:06 AM, Liisa Koski wrote: I am also getting the same error with my local biomart and local galaxy installations. Thanks, Liisa From: Jennifer Jackson j...@bx.psu.edu To: Christophe Klopp christophe.kl...@toulouse.inra.fr Cc: galaxy-user@lists.bx.psu.edu Date: 2011-05-31 09:32 Subject: Re: [galaxy-user] biomart error Sent by: galaxy-user-boun...@lists.bx.psu.edu Hello Christophe, I am unable to duplicate - BioMart appears to be functioning as expected this morning. Would you have time to run your query again? If the problem persists, if you could share your history with me (Options - Share or Publish - email back link) and list out the exact steps that you are performing, that would be very helpful. Best, Jen Galaxy team On 5/30/11 8:33 AM, Christophe Klopp wrote: Hi, I've tried a simple query in biomart : retrieve all gene locations for the Danio rerio in Ensembl 62 and I get an error : An error occurred running this job: /failure preparing job / The same happens with the test site? Cheers Christophe/ / -- = Christophe KLOPP BIAINRA Toulouse 31326 Castanet-Tolosan = = Tel: 33 5 61 28 50 36 Email:christophe.kl...@toulouse.inra.fr = =http://www.sigenae.org/ = =http://bioinfo.genotoul.fr/ = ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should
Re: [galaxy-user] Removing deleted datasets
Simon, In order for a dataset file to be removed from disk, no active library associations (LibraryDatasetDatasetAssociations) or history associations (HistoryDatasetAssociations) can be pointing to it. When no active association objects are pointing to a dataset file, it will ultimate be removed from disk via option -3 (the purge_datasets option) in the cleanup_datasets.py script. However, another factor in removing the file from disk is that the configured number of days must have passed since everything pointing to the file was marked as deleted. The default number of days in the script is 60. To remove files from disk on the same day they were marked as deleted, override the default by setting the -d flag to 0. Greg Von Kuster On Apr 30, 2011, at 4:59 PM, Simon Lank wrote: Hi. Our current galaxy database is ~ 600 gb, most of which are user deleted datasets. I followed the instructions here: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDatasets and ran the shell scripts in recommended order. One of them in particular (I think it was purge_histories.sh) took amost 24 hours to complete. However, it doesn't appear any / most of the files were actually deleted, since we still have ~ 600 gb of dataset files. Is there something obvious I can try to get the files purged correctly? Thanks. Simon Simon Lank Research Specialist O'Connor Lab, WNPRC 555 Science Dr. Madison WI (608) 265-3389 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] biomart plugin
Hello Andrea, Make a copy of the ~/tools/data_source/biomart.xml for your local biomart install, and change the action in the following tag to point to it. inputs action=http://www.biomart.org/biomart/martview; check_values=false method=get target=_top Then add your new biomart tool wrapper to your tool_conf.xml file and start up your Galaxy instance. For details about adding a new tool, see https://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial. Greg Von Kuster On Mar 26, 2011, at 10:19 AM, Andrea Edwards wrote: Hello I have looked at the biomart plugin for Galaxy and this seems to allow access to marts on the biomart central server. Is there anyway to use this plugin to access a biomart on my server if I can't make my biomart available on the biomart central server. If not, would it be possible to achieve this with galaxy tools. I've heard of galaxy tools but never made one so I don;t know what is involved. Failing that would i be able to use the biomart plugin to access my server if I had a local installation of galaxy thanks ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] library features
Thanks Belinda, On Mar 15, 2011, at 10:25 AM, Belinda M. Giardine wrote: I have been working with the libraries and found some features that would make things much easier. Sometimes files get loaded into the wrong folder, it would be nice to be able to move the file to another folder rather than delete and reload it. This feature has been implemented, but has not yet made it to our main server. Also the option of importing data into the library from a history is not available when updating a file. The work around is to load the new and delete the old, but you lose the history of the file changes that way. I'll fix this. Thanks, Belinda ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
