Errors running jobs in Galaxy 16.01 with slurm-drmaa 1.1.0
by Philip Blood
Hi Folks,
I'm trying to get an old instance of Galaxy (16.01) working for a user who
needs to use it this week for a class he is teaching (so upgrading Galaxy
is not an option at the moment). Due to a recent slurm upgrade on our
compute system to slurm 18.08.8, we had to replace the old slurm-drmaa
1.0.7 library <http://apps.man.poznan.pl/trac/slurm-drmaa>, which doesn't
work with with 18.08.8, with Nate's forked slurm-drmaa library version 1.1.0
<https://github.com/natefoo/slurm-drmaa>. That built fine with slurm
18.08.8 and (I think) we updated all the relevant pointers in the galaxy
config to point to the new slurm-drmaa 1.1.0 library.
However, now when I try to run jobs on our system I get errors (it worked
fine before with slurm-drmaa 1.0.7 and the older version of slurm). So, I
wanted to get a quick sanity check on whether this might be an issue with
trying to use the new slurm-drmaa with an old version of Galaxy, 16.01, or
if anyone has any other quick thoughts on troubleshooting this. The errors
I get are below.
Best,
Phil
*Short version (just the errors):*
198.91.54.159 - - [31/Aug/2019:16:31:28 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
*galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:30,366 (10)
drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job
error (2): No such file or directory*
198.91.54.159 - - [31/Aug/2019:16:31:32 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
*galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:35,372 (10)
drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job
error (0): No error*
198.91.54.159 - - [31/Aug/2019:16:31:37 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
*galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:40,377 (10)
drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job
error (0): No error*
198.91.54.159 - - [31/Aug/2019:16:31:41 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:31:45 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
*galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:45,383 (10)
drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job
error (0): No error*
198.91.54.159 - - [31/Aug/2019:16:31:49 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
*galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:50,388 (10)
drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job
error (0): No error*
198.91.54.159 - - [31/Aug/2019:16:31:53 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
*galaxy.jobs.runners.drmaa ERROR 2019-08-31 16:31:55,393 (10) All attempts
to submit job failed *
*Full context:*
198.91.54.159 - - [31/Aug/2019:16:30:27 +0000] "GET
/api/tools/squeue/build HTTP/1.1" 200 - "https://galaxy.bridges.psc.edu/"
"Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:68.0) Gecko/20100101
Firefox/68.0"
galaxy.tools DEBUG 2019-08-31 16:30:30,142 Validated and populated state
for tool request (4.081 ms)
galaxy.tools.actions INFO 2019-08-31 16:30:30,285 Handled output (100.616
ms)
galaxy.tools.actions INFO 2019-08-31 16:30:30,319 Verified access to
datasets (0.005 ms)
galaxy.tools.execute DEBUG 2019-08-31 16:30:30,368 Tool [squeue] created
job [10] (206.086 ms)
galaxy.tools.execute DEBUG 2019-08-31 16:30:30,376 Executed all jobs for
tool request: (233.862 ms)
198.91.54.159 - - [31/Aug/2019:16:30:30 +0000] "POST /api/tools HTTP/1.1"
200 - "https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0;
Win64; x64; rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:30:30 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
galaxy.jobs DEBUG 2019-08-31 16:30:30,747 (10) Working directory for job
is: /opt/packages/galaxy/galaxy01/database/job_working_directory/000/10
galaxy.jobs.handler DEBUG 2019-08-31 16:30:30,751 (10) Dispatching to slurm
runner
galaxy.jobs DEBUG 2019-08-31 16:30:30,774 (10) Persisting job destination
(destination id: LM4)
galaxy.jobs.runners DEBUG 2019-08-31 16:30:30,790 Job [10] queued (38.578
ms)
galaxy.jobs.handler INFO 2019-08-31 16:30:30,818 (10) Job dispatched
galaxy.tools.deps DEBUG 2019-08-31 16:30:31,012 Building dependency shell
command for dependency 'slurm'
galaxy.tools.deps DEBUG 2019-08-31 16:30:31,013 Find dependency slurm
version None
galaxy.tools.deps DEBUG 2019-08-31 16:30:31,013 Resolver tool_shed_packages
returned <galaxy.tools.deps.resolvers.NullDependency object at 0x1b38390>
(isnull? True)
galaxy.tools.deps DEBUG 2019-08-31 16:30:31,014 Resolver galaxy_packages
returned
<galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object
at 0x7fc78c334750> (isnull? False)
galaxy.jobs.command_factory INFO 2019-08-31 16:30:31,057 Built script
[/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/tool_script.sh]
for tool
command[PACKAGE_BASE=/opt/packages/galaxy/galaxy01/tool_dependencies/slurm/18.08.8;
export PACKAGE_BASE; . /opt/packages/galaxy/galaxy0
1/tool_dependencies/slurm/18.08.8/env.sh; echo "hostname:" > output; echo "
" >> output; hostname >> output; echo " " >> output; env >> output; echo "
" >> output; date >> output; echo " " >> output; echo "Uptime:" >>
output; echo " " >> output; uptime >> output; echo " " >> output; echo
"Module
s:" >> output; echo " " >> output; module avail >> output 2>&1; echo " " >>
output; echo "SLURM Queue Status" >> output; echo " " >> output; echo "If
your job is running on the queues, it will be listed in the reports below:"
>> output; echo " " >> output; echo " " >> output; echo "Normal Report: s
queue" >> output; echo " " >> output; echo " " >> output; echo " " >>
output; squeue >> output; date >> output; echo " " >> output; echo " " >>
output; echo "*** Full Report: squeue -l ***" >> output; echo " " >>
output; squeue -l >> output; echo " " >> output; echo " " >> output; date
>> output;
echo " " >> output; echo "Local: ${LOCAL}" >> output; echo "Ramdisk:
${RAMDISK}" >> output; workdir=`pwd`; echo "workdir is $workdir" >> output;
cd $LOCAL; echo "i am in `pwd`" >> $workdir/output; cd $workdir; echo "i am
in `pwd`" >> output; date >> output; echo " " >> output]
galaxy.tools.deps DEBUG 2019-08-31 16:30:31,259 Building dependency shell
command for dependency 'samtools'
galaxy.tools.deps DEBUG 2019-08-31 16:30:31,259 Find dependency samtools
version None
galaxy.tools.deps DEBUG 2019-08-31 16:30:31,259 Resolver tool_shed_packages
returned <galaxy.tools.deps.resolvers.NullDependency object at 0x1b38390>
(isnull? True)
galaxy.tools.deps DEBUG 2019-08-31 16:30:31,279 Resolver galaxy_packages
returned
<galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object
at 0x7fc7b01e01d0> (isnull? False)
galaxy.jobs.runners DEBUG 2019-08-31 16:30:31,284 (10) command is:
/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/tool_script.sh;
return_code=$?; if [ -f
/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/output
] ; then cp /opt/packages/galaxy/galaxy01/databas
e/job_working_directory/000/10/output
/opt/packages/galaxy/galaxy01/database/files/000/dataset_10.dat ; fi;
PACKAGE_BASE=/opt/packages/galaxy/galaxy01/tool_dependencies/samtools/0.1.19;
export PACKAGE_BASE; .
/opt/packages/galaxy/galaxy01/tool_dependencies/samtools/0.1.19/env.sh;
python "/opt/packa
ges/galaxy/galaxy01/database/job_working_directory/000/10/set_metadata_jGYkkM.py"
"/opt/packages/galaxy/galaxy01/tmp/tmpxmB5GA"
"/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/galaxy.json"
"/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/metadata_in_HistoryD
atasetAssociation_10_u2k7qq,/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/metadata_kwds_HistoryDatasetAssociation_10_2ZmSXR,/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/metadata_out_HistoryDatasetAssociation_10_shC78c,/opt/packages/galaxy/galaxy01/databa
se/job_working_directory/000/10/metadata_results_HistoryDatasetAssociation_10_57x96D,/opt/packages/galaxy/galaxy01/database/files/000/dataset_10.dat,/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/metadata_override_HistoryDatasetAssociation_10_AEeOfc"
5242880; sh -c "exit $retur
n_code"
galaxy.jobs.runners.drmaa DEBUG 2019-08-31 16:30:31,356 (10) submitting
file
/opt/packages/galaxy/galaxy01/database/job_working_directory/000/10/galaxy_10.sh
galaxy.jobs.runners.drmaa DEBUG 2019-08-31 16:30:31,356 (10) native
specification is: -p LM -C LM -N 1 -n 4 --ntasks-per-node=4 --mem=192500 -t
24:00:00
198.91.54.159 - - [31/Aug/2019:16:30:34 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:30:38 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:30:42 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:30:47 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:30:51 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:30:55 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:30:59 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:31:03 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:31:08 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:31:12 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:31:16 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:31:20 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:31:24 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:31:28 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
*galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:30,366 (10)
drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job
error (2): No such file or directory*
198.91.54.159 - - [31/Aug/2019:16:31:32 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
*galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:35,372 (10)
drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job
error (0): No error*
198.91.54.159 - - [31/Aug/2019:16:31:37 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
*galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:40,377 (10)
drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job
error (0): No error*
198.91.54.159 - - [31/Aug/2019:16:31:41 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
198.91.54.159 - - [31/Aug/2019:16:31:45 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
*galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:45,383 (10)
drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job
error (0): No error*
198.91.54.159 - - [31/Aug/2019:16:31:49 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
*galaxy.jobs.runners.drmaa WARNING 2019-08-31 16:31:50,388 (10)
drmaa.Session.runJob() failed, will retry: code 1: slurm_submit_batch_job
error (0): No error*
198.91.54.159 - - [31/Aug/2019:16:31:53 +0000] "GET
/api/histories/8237ee2988567c1c/contents HTTP/1.1" 200 - "
https://galaxy.bridges.psc.edu/" "Mozilla/5.0 (Windows NT 10.0; Win64; x64;
rv:68.0) Gecko/20100101 Firefox/68.0"
*galaxy.jobs.runners.drmaa ERROR 2019-08-31 16:31:55,393 (10) All attempts
to submit job failed *
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Hello and to whom it may concern.
As I point out in the matter, I am having trouble uploading information, particularly a BIOPROJECT that has already uploaded.
I am taking exactly the same steps that I previously used to load this database. I don't understand if Galaxy is not working properly today or what it can be.
I am loading it from: Download from web or upload from disk / Upload data as: Collection (s) / Load tabular data from: (pasted table).
Thank you in advance and sorry for the inconvenience
Lic. Rodrigo Machado
JTP Introducción a la Biología, TGG - UNER
Becario Doctoral
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?Hello,
Please could you help me to run this wrapper : RNA STAR Gapped-read mapper for RNA-seq data (Galaxy Version 2.7.2b)
without this error:
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::at
/galaxydata/galaxy-prod/my_job_working_directory/000/282/282124/tool_script.sh: line 9: 48744 Aborted (core dumped) STAR --runThreadN ${GALAXY_SLOTS:-4}...
Even if I increase the number of genome bins for coordinate-sorting, output files are all empty and I read this stderr above.
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Our team has multiple administrators to maintain the Galaxy platform in our cluster. And each administrator has their own account.
But we met a problem, terms of reference for each administrator is ambiguous. For example, if users report a bug in the platform, two or three administrators will handle it. But sometimes, these administrators can't discuss timely to determine who handles these problems (because they are in different time zones). So usually, they will try to fix the issue immediately when they get reports. But sometimes, their solution may conflict.
We try to arrange each administrator to handle one kind of issue to eliminate the conflict. But the reports cover lots of ranges. Our splitting can't work well. So we want to know if the galaxy can help us split the privilege of each admin accounts? Just let each admin account is in charge of developing one component of the galaxy. Such as A is in charge of tools uploading, B is in charge of fixing tools bug...
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by John Chilton
Dear Community,
The Galaxy Committers team is pleased to announce the release of Galaxy 19.09.
The release announcement for developers and admins can be found at
https://docs.galaxyproject.org/en/master/releases/19.09_announce.html
and user facing release notes are at
https://docs.galaxyproject.org/en/master/releases/19.09_announce_user.html.
A few release highlights are:
Interactive Tools
----------------------
A new type of Galaxy tool has been implemented that allows interactive
experiences like Galaxy Interactive Environments (via a proxy and
Docker containers) but using plugins defined with Galaxy’s XML tool
syntax.
Workflow Invocation Reports
---------------------------
Workflows may now define Markdown templates with Galaxy-specific
embedded syntax extensions that can tie together workflow inputs,
outputs, jobs, and metadata into rich reports.
New Toolshed Client Interface
-----------------------------
This project drove numerous enhancements to the Tool Shed API,
including vastly improved search functionality. This interface has
been completely re-imagined and feels much more interactive.
Check out the release notes for a lot more details - there are many
more enhancements such as new interface elements, visualizations,
datatypes, and more. There are also important notes for Galaxy
deployers - such as information about configuration changes in this
release and the formal deprecation of Python 2.7 support (this will be
the last release with formal support of Python 2).
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Hello,
As announced last month, there will be a GMOD codefest held before the
Plant and Animal Genome meeting in San Diego, January 9-10, 2020. The
meeting will be held at the Handlery hotel (down the street from the Town
and Country Hotel). Logistical and other information can be found at the
GMOD wiki as the details become more solid:
http://gmod.org/wiki/Codefest_2020
Several potential projects are described in this document:
https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-Vg...
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See you in San Diego!
Scott
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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Deleted Galaxy Account
by Horstmann, Cullen M
Good evening,
Upon trying to log onto my galaxy profile I received this message: "This account has been marked deleted, contact your local Galaxy administrator to restore the account." I was hoping I could re-gain access to this account because I have a lot of differential gene expression data on my account. Please let me know what I need to do to re-gain access at your earliest convenience.
Kind Regards,
Cullen Horstmann
Missouri State University
Master's in Biology
Graduate Researcher | Kim Lab
Teaching Assistant | Biology Department
1 year, 2 months
