Here's the official email announcement for the 2016 Galaxy Community
Conference. Please redistribute to any of your communities that would
benefit from attending.
Also please note:
* 1. Oral presentation abstracts are due March 25.*
2. The June 2016 GMOD Meeting
be held immediately after GCC2016.
The *2016 Galaxy Community Conference *(*GCC2016*, *gcc2016.iu.edu
<http://gcc2016.iu.edu/>*) features two days of presentations, discussions,
poster sessions, lightning talks, computer demos, keynotes, and
birds-of-a-feather meetups, *all about data-intensive biology and the tools
that support it*. Keynote speaker Yoav Gilad
<http://genes.uchicago.edu/directory/yoav-gilad-phd/>, a professor of human
genetics at the University of Chicago, will kick-start the main conference
with a discussion on the analysis of large gene regulatory data sets.
Preconference events include data
<https://gcc2016.iu.edu/hacks/hacks-data.php> and coding
<https://gcc2016.iu.edu/hacks/index.php>, and *two days of training*
<https://gcc16.sched.org/overview/type/Training+%E2%80%94+Any> in five
concurrent tracks covering 26 topics.
*GCC2016* will be held at *Indiana University* in Bloomington, Indiana,
June 25-29, 2016. Since it started seven years ago, GCC has been a
well-attended gathering of biologists, genome researchers,
bioinformaticians, and others in data-intensive biomedical research around
Galaxy <https://galaxyproject.org/> is an open, web-based platform for
data-intensive biomedical research and enables easy interactive analysis
through the web on arbitrarily large data sets. The Galaxy framework is a
major resource in achieving key research goals within the biological field.
It provides next-generation sequencing (NGS) tools and workflows for
short-read mapping, ChIP-seq, RNA-seq, metagenomics, variant analysis,
visualization, and support for Galaxy in the cloud. There are hundreds of
local installs, and *over 80 publicly accessible servers* around the world.
*Abstract submission** for oral presentations closes March 25. *Abstract
submission for posters and computer demonstrations closes May 20.
*Early registration* is now open. Registration starts at less than $45/day
for post-docs and students. Registering early assures you a place at the
conference and also a spot in the training workshops
<https://gcc16.sched.org/overview/type/Training+%E2%80%94+Any> you want to
attend. You can also *book conference housing* when you register. *Registration
and lodging scholarships* are available for attendees from underrepresented
groups and developing countries.
Thanks, and we hope to see you in Bloomington!
The *GCC2016 Exec*
Could somebody point me to a good explanation of how to setup and use GALAXY_SLOTS correctly on my server?
A basic explanation is good but I also make use of Pulsar to stage some jobs on our cluster here (my machine is 4-core and cluster I use is 12-core) so I am wondering if GALAXY_SLOTS can handle this (so I don't need to specify exact thread numbers in e.g. tool wrappers)
I'm having some difficulties with logging into my production website. I get
the following error message in the logs:
galaxy.web.framework.webapp WARNING 2016-04-06 18:47:41,852 User logged in
as 'userID' externally, but has a cookie as 'userID(a)vectorbase.org'
This started rather suddenly today after there was a space crisis on our
hard drive, which is the subject of my other recent email to this list.
We are using LDAP for external authentication. The same LDAP server is
being used by my "Pre" server, and logins are working fine. I've compared
both galaxy.ini and httpd.conf and can't find any discrepancies.
If someone has suggestions to offer, I would surely appreciate them.
Scott B. Szakonyi
*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
I'm trying to set our Galaxy instance to put Dataset and Temporary files on
a Symlinked drive, as there isn't sufficient room on the Galaxy server to
handle those files. However, I can't get it to work. Even though I've
changed these settings, Galaxy still seems to be creating large numbers of
files in our local database directory. Am I missing something here? I'm
including the relevant section of my galaxy.ini:
# -- Files and directories
# Dataset files are stored in this directory.
#file_path = database/files
file_path = /data/galaxy/database/files
# Temporary files are stored in this directory.
#new_file_path = database/tmp
new_file_path = /data/galaxy/tmp
Scott B. Szakonyi
*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
Just wonder where I can download the full sample file of dbkeys_list.yaml, which contents all the dbkeys and all DMs from the main tool shed. I'd appreciate if you would send me a copy. The sample file that comes with the ansible role only has a few lines.
Dear Galaxy Team,
1) Is there a bare-bones version of Galaxy available somewhere? That is, Galaxy with no tools pre-installed? We are creating Ansible play books for configuring Docker/Galaxy instances with our NLP tools installed. Currently we are using a fork of the Galaxy project with the bio tools removed, but this is less than ideal when we try to update to new versions of Galaxy.
Alternatively, does anyone have an automated process to delete unwanted tools that we could run immediately after cloning the main Galaxy repo?
2) Is is possible to either a) modify the existing upload tool, or b) implement a new upload tool? Several options in the upload tool do not make sense in our domain (e.g. selecting a genome) and we would also like to do some post-processing to files after they have been uploaded. I've looked at the code for the existing upload tool and it seems quite tightly coupled to the Galaxy code base. I was hoping the "Downgrade upload tool" thread from a few weeks ago was going to help, but unfortunately for me (and good for the user) they found a solution that didn't involve installing a new upload tool.
However, could I follow the approach suggested in that thread? I.E. go back in time and find an old upload.[py | xml] and use that as a starting point for my own custom upload tool? How far back in time would I have to go to find an upload.py that was a standalone tool?
Department of Computer Science
Dear Galaxy Team,
I'm trying to install the repeatexplorer tool
I get the following message that I cannot solve. it does not seem to be releated to the repeatexplorer tool itself since it is not using MPI as far as I can tell although it does not seem to happen with other tools at the galaxy instance.
ERROR: ld.so: object '/usr/lib/openmpi/lib/libmpi.so' from LD_PRELOAD cannot be preloaded (wrong ELF class: ELFCLASS64): ignored.
note: /usr/lib/openmpi/lib/libmpi.so exists and is a 64 bits lib
I've tried unsetting the LD_PRELOAD library for the galaxy user but that did not help,.
According to the logs it looks like this error occurs after the job finishes.
I would appreciate any clues on how to debug this and to find out where this message comes from.
below the snippet from the logfiles:
galaxy.jobs DEBUG 2016-04-04 11:22:40,544 (1829) Working directory for job is: /mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829
galaxy.jobs.handler DEBUG 2016-04-04 11:22:40,556 (1829) Dispatching to drmaa runner
galaxy.jobs DEBUG 2016-04-04 11:22:40,760 (1829) Persisting job destination (destination id: sge_default)
galaxy.jobs.runners DEBUG 2016-04-04 11:22:40,765 Job  queued (207.994 ms)
galaxy.jobs.handler INFO 2016-04-04 11:22:40,808 (1829) Job dispatched
galaxy.jobs.runners DEBUG 2016-04-04 11:22:41,841 (1829) command is: bash /mnt/data/home/NIOO/galaxy/galaxy-dist/tools/umbr_programs/seqclust/seqclust-main.sh -s /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3137.dat -m 0.01 -o 40 -d Viridiplantae -v /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3173.dat -w /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3174.dat -y /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3175.dat -z RMSKtable -r /mnt/data/home/NIOO/galaxy/galaxy-dist -t /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3176.dat -u '/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/dataset_3176_files' -p false -f 0 -a True -l 55 -x " " -K 10; return_code=$?; python "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/set_metadata_VcdaXP.py" "/tmp/tmpOOJhc4" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/galaxy.json" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2937_ivd_QV,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2937__9U8lt,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2937_zmXF2T,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2937_XHZd2p,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3176.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2937_0_rQHI" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2936_2FIF61,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2936__PZplz,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2936_ImcuR2,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2936_Jm3zxC,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3175.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2936_qkgfR7" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2935_5Ozbvu,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2935_H_7TWw,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2935_Rp42fp,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2935_ycng_Q,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3174.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2935_gbk6Im" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2934_wM1GtU,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2934_pUrJqr,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2934__8Jvh6,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2934_n_AZt2,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3173.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2934_ovKSAZ" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:22:41,890 (1829) submitting file /mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/galaxy_1829.sh
galaxy.jobs.runners.drmaa INFO 2016-04-04 11:22:41,900 (1829) queued as 9507
galaxy.jobs DEBUG 2016-04-04 11:22:41,950 (1829) Persisting job destination (destination id: sge_default)
galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:22:42,159 (1829/9507) state change: job is queued and active
galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:22:44,286 (1829/9507) state change: job is running
galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:47:59,005 (1829/9507) state change: job finished normally
galaxy.jobs DEBUG 2016-04-04 11:47:59,500 setting dataset state to ERROR
galaxy.jobs DEBUG 2016-04-04 11:47:59,527 setting dataset state to ERROR
galaxy.jobs DEBUG 2016-04-04 11:47:59,559 setting dataset state to ERROR
galaxy.jobs DEBUG 2016-04-04 11:47:59,602 setting dataset state to ERROR
galaxy.jobs INFO 2016-04-04 11:47:59,779 Collecting job metrics for <galaxy.model.Job object at 0x7f3f346d89d0>
galaxy.jobs DEBUG 2016-04-04 11:47:59,798 job 1829 ended (finish() executed in (595.557 ms))
We just ran into a Tool Shed installation problem under a test
installation of Galaxy v16.01, while trying to install the meme_fimo
Clicking through the GUI takes me to the failed install of the
perl_xml_parser_expat version 2.41 package (under
The Admin GUI shows this long stack trace error:
line 123, in install_and_build_package_via_fabric
tool_dependency = self.install_and_build_package(
install_environment, tool_dependency, actions_dict )
line 81, in install_and_build_package
line 31, in execute_step
line 1253, in execute_step
line 140, in handle_command
line 390, in set_tool_dependency_attributes
line 150, in do
return getattr(self.registry(), name)(*args, **kwargs)
line 187, in execute
query = query % tuple([db.literal(item) for item in args])
line 278, in literal
return self.escape(o, self.encoders)
line 208, in unicode_literal
'latin-1' codec can't encode character u'\u2018' in position 1070:
ordinal not in range(256)
This is the left single quotation mark (U+2018), which I think comes
from the failed installation log:
$ tail /mnt/shared/galaxy/tool_dependency_dir/perl_xml_parser_expat/2.41/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9/INSTALLATION.log
Expat.xs:2179: error: ‘parser’ undeclared (first use in this function)
Expat.xs:2180: error: ‘CallbackVector’ has no member named ‘st_serial’
Expat.xs:2182: error: ‘CallbackVector’ has no member named ‘skip_until’
Expat.c: In function ‘XS_XML__Parser__Expat_Do_External_Parse’:
Expat.c:2904: error: ‘XML_Parser’ undeclared (first use in this function)
Expat.c:2904: error: expected ‘;’ before ‘parser’
Expat.xs:2194: error: ‘parser’ undeclared (first use in this function)
make: *** [Expat.o] Error 1
make: *** [subdirs] Error 2
Note those fancy quote characters? Yep:
$ hexdump -C /mnt/shared/galaxy/tool_dependency_dir/perl_xml_parser_expat/2.41/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9/INSTALLATION.log
| tail -n 15
00022e90 6f 72 3a 20 65 78 70 65 63 74 65 64 20 e2 80 98 |or: expected ...|
00022ea0 3b e2 80 99 20 62 65 66 6f 72 65 20 e2 80 98 70 |;... before ...p|
00022eb0 61 72 73 65 72 e2 80 99 0a 45 78 70 61 74 2e 78 |arser....Expat.x|
00022ec0 73 3a 32 31 39 34 3a 20 65 72 72 6f 72 3a 20 e2 |s:2194: error: .|
00022ed0 80 98 70 61 72 73 65 72 e2 80 99 20 75 6e 64 65 |..parser... unde|
00022ee0 63 6c 61 72 65 64 20 28 66 69 72 73 74 20 75 73 |clared (first us|
00022ef0 65 20 69 6e 20 74 68 69 73 20 66 75 6e 63 74 69 |e in this functi|
00022f00 6f 6e 29 0a 6d 61 6b 65 5b 31 5d 3a 20 2a 2a 2a |on).make: ***|
00022f10 20 5b 45 78 70 61 74 2e 6f 5d 20 45 72 72 6f 72 | [Expat.o] Error|
00022f20 20 31 0a 6d 61 6b 65 3a 20 2a 2a 2a 20 5b 73 75 | 1.make: *** [su|
00022f30 62 64 69 72 73 5d 20 45 72 72 6f 72 20 32 0a 23 |bdirs] Error 2.#|
00022f40 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 |################|
00022f60 23 23 23 23 23 23 23 23 23 23 23 23 0a |############.|
Notice the sequence in hex of e2 80 98, that's the UTF-8 (hex) for the
problem character. We also have e2 80 99 which is the matching right
While I can go over the full INSTALLATION.log to work out what might
be wrong, there is clearly a Galaxy problem with the UTF-8 encoded
character. Going over the Galaxy mailing list there have been similar
problems (although not ToolShed related) reported in the past (2013)
with MySQL and the table encodings:
Are there still known issues with encodings and the MySQL galaxy schema?
Are we likely to run into other corner cases with MySQL where we would
be better off switching to PostgreSQL?
Hey guys, today I updated to the latest version of galaxy. No I noticed
that because of the new virtualenv/wheel startup procedure, the init
scripts as mentioned here
are not working anymore. Whet is the new startup procedure?
Central Veterinary Institute of Wageningen UR (CVI)
Department of Infection Biology
PO box 65, 8200 AB Lelystad, NL
Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad