Please help fix toolshed repository: trtr
by Lance Parsons
I was helping someone with their toolshed repository and we ran into an
issue, there is an old folder "myTools" in the repository that we cannot
delete. It has a second copy of the tool (inadvertently). However, when
we upload a new version with Planemo, the directory remains. Attempts to
delete it via the toolshed web interface result in internal server
errors. Can an admin take a look?
https://toolshed.g2.bx.psu.edu/view/mrvollger/trtr/13cad5d36301
--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
Princeton University
5 years, 8 months
Help with dynamic job destination
by Lance Parsons
I'm trying to setup a dynamic job destination for bowtie2 so that it
submits to a different destination if the `-a` option is set or the `-k`
option is set to a high value. I've got things working, but the function
I've written seems rather complicated and ugly. I was wondering if
anyone had any advice on a better way to query job parameters. See the
function here:
https://gist.github.com/lparsons/a4724b51afd9027e3c0e
Thanks in advance for any suggestions or comments.
--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
Princeton University
5 years, 8 months
Job stuck in running state.
by Zuzanna K. Filutowska
Dear All,
I am running newest version of Galaxy with PBS and I am observing
strange behaviour: some jobs that were finished on the queue system are
still shown as running on Galaxy Web interface. Communication with PBS
server seems to work fine all the time. Nothing interesting seems to be
in logs despite debug being on:
sqlalchemy.pool.QueuePool ERROR 2016-03-13 11:36:02,544 Error closing
cursor
Any ideas, what can be a problem?
--
Pozdrawiam,
--
Zuzanna K. Filutowska, HPC Systems Administrator
Poznan Supercomputing and Networking Center
Institute of Bioorganic Chemistry Polish Academy of Sciences
Seize the day boys! Make your lifes extraordinary! --John Keating
5 years, 8 months
Re: [galaxy-dev] Trackster in 16.01 broken
by Marius van den Beek
Hi Lubos,
I opened a Pull Request on https://github.com/galaxyproject/galaxy/pull/1930,
which should hopefully fix the problem.
If you want to give it a try, you can do
`git fetch origin pull/1930/head:more_bytestring_for_pysam`
and
`git checkout more_bytestring_for_pysam`.
When the problem has been solved, you can switch back to release_16.01 by
doing `git checkout release_16.01`.
Thanks for reporting the error,
Marius
On 15 March 2016 at 19:25, Marius van den Beek <m.vandenbeek(a)gmail.com>
wrote:
> Yes, `git checkout release_16.01` should do it, but wait a second, there
> might actually be a problem,
> since ` File "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
> line 892, in get_iterator`,
> while the PR addresses 354-356!
>
>
> On 15 March 2016 at 19:23, Lubos Klucar <klucar(a)embnet.sk> wrote:
>
>>
>>
>> On 15. 3. 2016 19:15, Marius van den Beek wrote:
>>
>>> Hi Lubos,
>>>
>>> hmm, I'm surprised about this.
>>> Just to make sure, you are on the release_16.01 branch?
>>> (`git branch` should highlight release_16.01)
>>> This PR hasn't been merged into dev yet.
>>>
>>>
>> Hi Marius,
>>
>> it seems I need more help with git, not the Galaxy!. ;-) My git branch
>> gives me:
>>
>> dev
>> * master
>>
>> How should I 'switch' to 16.01??..
>>
>> regards
>>
>> Lubos
>>
>> Cheers,
>>> Marius
>>>
>>> On 15 March 2016 at 19:08, Lubos Klucar <klucar(a)embnet.sk
>>> <mailto:klucar@embnet.sk>> wrote:
>>>
>>> Dear Marius,
>>>
>>> thanks for help, but it looks our galaxy is up to date:
>>>
>>> remote: Counting objects: 111, done.
>>> remote: Compressing objects: 100% (23/23), done.
>>> remote: Total 111 (delta 82), reused 75 (delta 75), pack-reused 13
>>> Receiving objects: 100% (111/111), 39.85 KiB, done.
>>> Resolving deltas: 100% (82/82), completed with 29 local objects.
>>> >From https://github.com/galaxyproject/galaxy
>>> 8423fe7..23c3300 dev -> origin/dev
>>> 5a50a46..65a5b08 release_16.01 -> origin/release_16.01
>>> Already up-to-date.
>>>
>>> After Galaxy restart the problem still persist...
>>>
>>> all the best
>>>
>>> Lubos
>>>
>>> On 15. 3. 2016 18:59, Marius van den Beek wrote:
>>>
>>> Hello Lubos,
>>>
>>> this should be fixed with
>>> https://github.com/galaxyproject/galaxy/pull/1897.
>>> If you pull in the latest changes (git pull) on the
>>> release_16.01 branch
>>> things should work again.
>>>
>>> Cheers,
>>> Marius
>>>
>>> On 15 March 2016 at 18:54, Lubos Klucar <klucar(a)embnet.sk
>>> <mailto:klucar@embnet.sk>
>>> <mailto:klucar@embnet.sk <mailto:klucar@embnet.sk>>> wrote:
>>>
>>> Hi,
>>>
>>> after upgrading from 15.10 to 16.01, the trackster
>>> visualisation
>>> tool is partly defective. It can successfully show e.g. GFF
>>> tracks,
>>> but after adding e.g. BAM track nothing is shown. The only
>>> suspicious debug output I could get when loading
>>> non-working-track is:
>>>
>>> galaxy.webapps.galaxy.api.datasets ERROR 2016-03-15
>>> 11:44:38,853
>>> Error in dataset API at listing contents: Expected bytes,
>>> got
>>> unicode: Expected bytes, got unicode
>>> Traceback (most recent call last):
>>> File
>>>
>>>
>>> "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py",
>>> line 66, in show
>>> rval = self._data( trans, dataset, **kwd )
>>> File
>>>
>>>
>>> "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py",
>>> line 235, in _data
>>> ref_seq=region, mean_depth=mean_depth, **kwargs )
>>> File
>>>
>>>
>>> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
>>> line 192, in get_data
>>> iterator = self.get_iterator( data_file, chrom, start,
>>> end,
>>> **kwargs )
>>> File
>>>
>>>
>>> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
>>> line 892, in get_iterator
>>> data = data_file.fetch( start=start, end=end,
>>> reference=chrom )
>>> File "pysam/calignmentfile.pyx", line 868, in
>>> pysam.calignmentfile.AlignmentFile.fetch
>>> (pysam/calignmentfile.c:10170)
>>> File "pysam/calignmentfile.pyx", line 787, in
>>> pysam.calignmentfile.AlignmentFile.parse_region
>>> (pysam/calignmentfile.c:9605)
>>> File "pysam/calignmentfile.pyx", line 1576, in
>>> pysam.calignmentfile.AlignmentFile.gettid
>>> (pysam/calignmentfile.c:16665)
>>> File "pysam/calignmentfile.pyx", line 640, in
>>> pysam.calignmentfile.AlignmentFile.get_tid
>>> (pysam/calignmentfile.c:8208)
>>> File "pysam/cutils.pyx", line 106, in
>>> pysam.cutils.force_bytes
>>> (pysam/cutils.c:2170)
>>> TypeError: Expected bytes, got unicode
>>>
>>> Any help to solve this problem would be highly appreciated!
>>>
>>> many thanks
>>> --
>>>
>>> Lubos Klucar
>>> ___________________________________________________________
>>> 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:
>>> https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/mailinglists/
>>>
>>>
>>>
>>> --
>>>
>>> Lubos Klucar
>>>
>>> Institute of Molecular Biology
>>> Slovak Academy of Science
>>> Dubravska cesta 21
>>> 845 51 Bratislava 45
>>> Slovakia
>>>
>>> Tel.: +421 2 5930 7413
>>> <tel:%2B421%202%205930%207413>
>>> Fax.: +421 2 5930 7416
>>> <tel:%2B421%202%205930%207416>
>>>
>>>
>>>
>> --
>>
>> Lubos Klucar
>>
>> Institute of Molecular Biology
>> Slovak Academy of Science
>> Dubravska cesta 21
>> 845 51 Bratislava 45
>> Slovakia
>>
>> Tel.: +421 2 5930 7413
>> Fax.: +421 2 5930 7416
>>
>
>
5 years, 8 months
Trackster in 16.01 broken
by Lubos Klucar
Hi,
after upgrading from 15.10 to 16.01, the trackster visualisation tool is
partly defective. It can successfully show e.g. GFF tracks, but after
adding e.g. BAM track nothing is shown. The only suspicious debug output
I could get when loading non-working-track is:
galaxy.webapps.galaxy.api.datasets ERROR 2016-03-15 11:44:38,853 Error
in dataset API at listing contents: Expected bytes, got unicode:
Expected bytes, got unicode
Traceback (most recent call last):
File
"/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py", line
66, in show
rval = self._data( trans, dataset, **kwd )
File
"/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py", line
235, in _data
ref_seq=region, mean_depth=mean_depth, **kwargs )
File
"/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
line 192, in get_data
iterator = self.get_iterator( data_file, chrom, start, end, **kwargs )
File
"/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py",
line 892, in get_iterator
data = data_file.fetch( start=start, end=end, reference=chrom )
File "pysam/calignmentfile.pyx", line 868, in
pysam.calignmentfile.AlignmentFile.fetch (pysam/calignmentfile.c:10170)
File "pysam/calignmentfile.pyx", line 787, in
pysam.calignmentfile.AlignmentFile.parse_region
(pysam/calignmentfile.c:9605)
File "pysam/calignmentfile.pyx", line 1576, in
pysam.calignmentfile.AlignmentFile.gettid (pysam/calignmentfile.c:16665)
File "pysam/calignmentfile.pyx", line 640, in
pysam.calignmentfile.AlignmentFile.get_tid (pysam/calignmentfile.c:8208)
File "pysam/cutils.pyx", line 106, in pysam.cutils.force_bytes
(pysam/cutils.c:2170)
TypeError: Expected bytes, got unicode
Any help to solve this problem would be highly appreciated!
many thanks
--
Lubos Klucar
5 years, 8 months
Problems uploading files to galaxy
by Lemley, Rob
Hi,
I'm hoping you can help out with a problem we are experiencing uploading files to our own Galaxy instance.
When a user tries to upload a file to Galaxy through their web browser, the job errors out:
Traceback (most recent call last):
File "/gpfs/fs1/sfw/cibem_galaxy/app/galaxy/tools/data_source/upload.py", line 430, in <module>
__main__()
File "/gpfs/fs1/sfw/cibem_galaxy/app/galaxy/tools/data_source/upload.py", line 407, in __main__
for line in open( sys.argv[3], 'r' ):
IOError: [Errno 13] Permission denied: '/scratch/XXXXXX/XXXXXX/galaxy/tmp/tmpSlG2pC'
The permissions on the referenced file:
-rw-------+ 1 rlemley rlemley 317 Mar 7 13:42 tmpSlG2pC
As the Galaxy daemons run as XXXXXX_galaxy, it does not have permission to read the file.
I tried modifying external_chown_script.py so that XXXXXX_galaxy has permission to read that file, but that caused problems elsewhere so I backed out the changes.
Any suggestions?
Many thanks,
-Rob
Rob Lemley
Systems Administrator - CIRC
University of Rochester
5 years, 8 months
Tool-install error with yaml file
by Rathert, Philipp, Dr.
Dear all,
I want to install a bunch of tools using the install-tools
function. In my yaml file tool.yml i have specified the url if my docker
instance wit the ip adress i use in the web browser and the api_key is admin
When i run install-tools tool.yml I get the error below and nothing happens.
I attached my tool.yml file in case the error comes from there.
Anybody has an idea whats wrong?
root@galaxy:/galaxy-central# install-tools tool.yml * Starting PostgreSQL
9.3 database server [ OK ] starting Galaxy Activating virtualenv at .venv
Ignoring indexes: https://pypi.python.org/simple
/galaxy-central/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315:
SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name
Indication) extension to TLS is not available on this platform. This may
cause the server to present an incorrect TLS certificate, which can cause
validation failures. For more information, see
https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.
SNIMissingWarning
/galaxy-central/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120:
InsecurePlatformWarning: A true SSLContext object is not available. This
prevents urllib3 from configuring SSL appropriately and may cause certain
SSL connections to fail. For more information, see
https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformw....
InsecurePlatformWarning Requirement already up-to-date: pip==8.0.2+gx2 in
./.venv/lib/python2.7/site-packages Requirement already satisfied
(use --upgrade to upgrade): bx-python==0.7.3 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2))
Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3))
Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))
Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))
Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7))
Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))
Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9))
Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16))
Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17))
Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18))
Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19))
Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20))
Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21))
Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22))
Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23))
Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24))
Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25))
Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26))
Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27))
Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30))
Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31))
Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34))
Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35))
Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36))
Requirement already satisfied (use --upgrade to upgrade):
requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 37)) Requirement already satisfied (use --upgrade to
upgrade): kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 40)) Requirement already satisfied (use --upgrade to
upgrade): amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 41)) Requirement already satisfied (use --upgrade to
upgrade): anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r
requirements.txt (line 42)) Requirement already satisfied (use --upgrade to
upgrade): sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages
(from -r requirements.txt (line 45)) Requirement already satisfied
(use --upgrade to upgrade): decorator==4.0.2 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 46))
Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 47))
Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48))
Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49))
Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51))
Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 52))
Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 53))
Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54))
Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 57))
Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 58))
Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59))
Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66))
Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1
in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 69))
You are using pip version 8.0.2+gx2, however version 8.1.0 is available. You
should consider upgrading via the 'pip install --upgrade pip' command.
Requirement already satisfied (use --upgrade to upgrade): psycopg2==2.6.1 in
./.venv/lib/python2.7/site-packages (from -r /dev/stdin (line 1))
Requirement already satisfied (use --upgrade to upgrade): drmaa in
./.venv/lib/python2.7/site-packages (from -r /dev/stdin (line 2)) You are
using pip version 8.0.2+gx2, however version 8.1.0 is available. You should
consider upgrading via the 'pip install --upgrade pip' command. Activating
virtualenv at .venv Daemon is already running (PID: 323 from PID file
galaxy_install.pid) Galaxy is running.
PLAY *************************
TASK [galaxy_tools : include] **************** skipping: [localhost]
TASK [galaxy_tools : include] **************** included:
/home/galaxy/ansible/galaxy-tools-playbook/roles/galaxy_tools/tasks/tools.yml
for localhost
TASK [galaxy_tools : Create/invoke script virtualenv] ******** fatal:
[localhost]: UNREACHABLE! => {"changed": false, "msg": "All items
completed", "results": [{"item": "pyyaml", "msg": "Authentication or
permission failure. In some cases, you may have been able to authenticate
and did not have permissions on the remote directory. Consider changing the
remote temp path in ansible.cfg to a path rooted in \"/tmp\". Failed command
was: ( umask 22 && mkdir -p \"echo
$HOME/.ansible/tmp/ansible-tmp-1457708936.13-72771790334072\" && echo \"echo
$HOME/.ansible/tmp/ansible-tmp-1457708936.13-72771790334072\" ), exited with
result 1", "unreachable": true}, {"item": "bioblend", "msg": "Authentication
or permission failure. In some cases, you may have been able to authenticate
and did not have permissions on the remote directory. Consider changing the
remote temp path in ansible.cfg to a path rooted in \"/tmp\". Failed command
was: ( umask 22 && mkdir -p \"echo
$HOME/.ansible/tmp/ansible-tmp-1457708936.15-89736978480357\" && echo \"echo
$HOME/.ansible/tmp/ansible-tmp-1457708936.15-89736978480357\" ), exited with
result 1", "unreachable": true}]} to retry, use: --limit @tools.retry
PLAY RECAP *********************** localhost : ok=1 changed=0 unreachable=1
failed=0
5 years, 8 months
external_chown_script.py and the local job runner
by Peter Cock
On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
> Hello all,
>
> We're currently looking at changing our Galaxy setup to link user accounts
> with Linux user accounts for better cluster integration (running jobs as the
> actual user on SGE). As part of this, we've tried setting up a fresh
> installation on a new VM which has thrown up some issues.
>
> [snip]
We eventually got Galaxy to talk to SGE and submit jobs successfully
as the individual user's Linux account, with external_chown_script.py
being called to handle ownership of the files.
However, we would like to have some jobs (like the upload tool)
configured to run on the Galaxy server itself - and the easiest way
to do that is via the local job runner.
We tried both the "upload1" and "Convert characters1" tools. These
jobs would start and seem to run, but then fail with a file permission
error (I don't have a stack trace to hand). From watching the Galaxy
terminal output from run.sh we could see external_chown_script.py
being called.
As a test, when we disabled the external_chown_script setting in
config/galaxy.ini then the local jobs would work.
When using the local job runner, does Galaxy run the child process
as the Galaxy user (my guess - no chown needed), or as the job
owner's Linux account (calling chown would be needed)?
Thanks,
Peter
5 years, 8 months
Mapping users to slurm
by Pardo Diaz, Alfonso
Hello,
I have connected my galaxy to a Slurm cluster via DRMAA. Galaxy can send jobs to the cluster without problems. But then I configure galaxy to use “real users” I got this error:
"User myuser(a)mydomain.es<mailto:myuser@mydomain.es> is not mapped to any real user, and not permitted to start jobs”
Could you help me?
Tanks!!
This is my job_con.xml:
<?xml version="1.0"?>
<job_conf>
<plugins workers="6">
<plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="2">
<param id="drmaa_library_path">/opt/slurm-drmaa/lib/libdrmaa.so</param>
</plugin>
</plugins>
<handlers default="handlers">
<handler id="main" tags="handlers"/>
</handlers>
<destinations default="drmaa">
<destination id="drmaa" runner="drmaa">
<param id="galaxy_external_runjob_script">/opt/galaxy/scripts/drmaa_external_runner.py</param>
<param id="galaxy_external_killjob_script">/opt/galaxy/scripts/drmaa_external_killer.py</param>
<param id="galaxy_external_chown_script">/opt/galaxy/scripts/external_chown_script.py</param>
</destination>
</destinations>
</job_conf>
this is my auth_conf.xml:
<?xml version="1.0"?>
<auth>
<authenticator>
<type>ldap</type>
<options>
<auto-register>True</auto-register>
<allow-password-change>False</allow-password-change>
<server>ldap://ldap.ceta-ciemat.es</server>
<login-use-username>True</login-use-username>
<continue-on-failure>False</continue-on-failure>
<search-filter>(|(mail={email})(uid={username}))</search-filter>
<search-fields>uid,mail,dn</search-fields>
<search-base>ou=xxxxxx,dc=xxxxx,dc=xxxxx</search-base>
<bind-user>{dn}</bind-user>
<bind-password>{password}</bind-password>
<auto-register-username>{uid}</auto-register-username>
<auto-register-email>{mail}</auto-register-email>
<login-use-username>True</login-use-username>
</options>
</authenticator>
<authenticator>
<type>localdb</type>
<options>
<!-- Whether users are allowed to change their password. Default is
False. -->
<allow-password-change>true</allow-password-change>
</options>
</authenticator>
</auth>
And this is my galaxy.ini:
[server:main]
port = 8080
host = 0.0.0.0
use_threadpool = True
threadpool_kill_thread_limit = 10800
[filter:gzip]
[filter:proxy-prefix]
prefix = /galaxy
[app:main]
paste.app_factory = galaxy.web.buildapp:app_factory
database_connection = postgres://xxxxxxxx:xxxxxx@xxxxx/galaxy_project
database_engine_option_server_side_cursors = True
database_engine_option_strategy = threadlocal
new_file_path = database/tmp
tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml
tool_dependency_dir = dependency_dir
cluster_files_directory = database/pbs
smtp_server = localhost
use_nglims = False
nglims_config_file = tool-data/nglims.yaml
debug = true
use_interactive = True
require_login = True
allow_user_creation = False
allow_user_deletion = True
allow_user_impersonation = True
allow_user_dataset_purge = True
new_user_dataset_access_role_default_private = True
auth_config_file = config/auth_conf.xml
enable_quotas = True
expose_dataset_path = False
job_config_file = config/job_conf.xml
enable_job_recovery = True
outputs_to_working_directory = True
drmaa_external_runjob_script = scripts/drmaa_external_runner.py
drmaa_external_killjob_script = scripts/drmaa_external_killer.py
external_chown_script = scripts/external_chown_script.py
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5 years, 8 months
