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Lucille Delisle
@lldelisle
Thanks, indeed it worked.
github-ic
@github-ic
@natefoo:matrix.org
We can't around this error - any idea what might be the problem?
job.c: In function ‘slurmdrmaa_job_control’:
job.c:117:8: error: too few arguments to function ‘slurm_kill_job2’
if(slurm_kill_job2(self->job_id, SIGKILL, 0) == -1) {
^~~~~~~
In file included from ../slurm_drmaa/job.h:29,
from job.c:38:
/usr/include/slurm/slurm.h:3531:12: note: declared here
extern int slurm_kill_job2(const char *job_id, uint16_t signal, uint16_t flags,
Nate Coraor
@natefoo:matrix.org
[m]
It's fixed, I need to create a new slurm-drmaa release.
If you have the GNU autotools installed you can clone the main branch and run ./autogen.sh followed by the usual ./configure, make, etc.
You need ragel and gperf as well.
If not I should be able to create a release today or tomorrow some time.
github-ic
@github-ic
we will try the ragel and gperf
Nate Coraor
@natefoo:matrix.org
[m]
autodist.sh can do it for you in Docker if you would prefer that to installing system packages.
github-ic
@github-ic

We installed ragel and gperf but get these errors.

./autogen.sh
running sh autogen.sh (/usr/local/slurm-drmaa/drmaa_utils)
sh: autogen.sh: No such file or directory

./configure
=== configuring in drmaa_utils (/usr/local/slurm-drmaa/drmaa_utils)
configure: WARNING: no configuration information is in drmaa_utils

make
make[2]: Entering directory '/usr/local/slurm-drmaa/drmaa_utils'
make[2]: * No rule to make target 'all'. Stop

Nate Coraor
@natefoo:matrix.org
[m]
You may've missed doing a recursive clone, drmaa_utils is a separate repo. You can fix that with git submodule init && git submodule update
23 replies
However, I have just published a new release: https://github.com/natefoo/slurm-drmaa/releases/tag/1.1.3
github-ic
@github-ic
Thanks!
thepineapplepirate
@thepineapplepirate
is the EU server down?
its's under heavy load
thepineapplepirate
@thepineapplepirate
Ok, thanks!
github-ic
@github-ic
But when we restart galaxy since we are using slurm the jobs will continue running?
Nate Coraor
@natefoo:matrix.org
[m]
Correct
seahu1
@seahu1
Hello, when I click"ALL workflows"on https://usegalaxy.org/,it tells
Hello, when I click"ALL workflows"on https://usegalaxy.org/,it tells "You must be logged in with proper credentials to make this request." How can I log in? I can't find any key.
Nicola Soranzo
@nsoranzo:matrix.org
[m]
@seahu1: Click on "Login or Register" in the top menu
Damla Aygün
@aygun09_gitlab
Hello, I'm trying to upload a whole exome data (fastq) by using FileZilla. I watched tutorial for ftp here > https://galaxyproject.org/ftp-upload/ but in there I have a problem; there is a mismatch between certificate fingerprints what I am viewing from your website and what filezilla is showing. How can I solve that?
6 replies
Helena Rasche
@hexylena:matrix.org
[m]
Glad it worked ok! Good luck
1 reply
pdagosto
@pdagosto
We have had a disk space issue on our Galaxy server after loading some data into the database. We have another location with enough disk space to accommodate the database but I have some questions.
  1. Is the default database SQLite or some DB server (e.g.,postgres).
1 reply
  1. Is it safe to move the database after shutting down Galaxy?
  2. Can we tell Galaxy where the database resides?
1 reply
We're using the default (out of the box) config. We didn't do anything special to install postgres. Would that not result in teh DB being SQLite?
1 reply
David Hong
@hong7734_gitlab
I have been using Galaxy (server name:http://131.247.66.74:8080/) but recently I got an error but our university IT guy wants me to contact Galaxy admins. So Galaxy does not support this server anymore?
8 replies
Christophe Antoniewski
@drosofff
Hey ! I just found by chance a junk tool in the main https://toolshed.g2.bx.psu.edu/ : buyhoverboardsuk
Martin Cech
@martenson
@drosofff thanks for the reporting, I got rid of it.
Asaduzzaman Asad
@zasamanzud:matrix.org
[m]
Hi there, I need some help regarding the addition of a reference sequence (Campylobacter jejuni) in the galaxy database. Can anyone help me out here, please?
1 reply
gluatuno
@gluatuno
I wonder how to covert embl format to fasta format on galaxy. Thanks!
1 reply
basic99
@basic99
@natefoo:matrix.org I am helping github-ic install slurm. It is working but need to change slurm.comf. Can this be done without losing jobs and workflow currently running?
2 replies
Thielyfabian
@Thielyfabian
Why can't I add data on the platform anymore? data that before I remove them?
dannon
@dannon:matrix.org
[m]
@Thielyfabian: Is your quota full?
Thielyfabian
@Thielyfabian
@dannon:matrix.org no, it's 0%, but I can't add anything with more than 1.0G
dannon
@dannon:matrix.org
[m]
Which Galaxy server is this? And, you're logged in, right?
Thielyfabian
@Thielyfabian
I'm using https://usegalaxy.eu/, I'm logged in.
Björn Grüning
@bgruening
@Thielyfabian please use the FTP server https://galaxyproject.eu/ftp/
Thielyfabian
@Thielyfabian
@bgruening can you explain me in detail how to use? or indicate me a tutorial for this?
bgruening
@bgruening:matrix.org
[m]
everything is linked on that page above. Here are instructions to use the FTP https://galaxyproject.org/ftp-upload/
are you using Windows?
Thielyfabian
@Thielyfabian
yes
Björn Grüning
@bgruening
maybe your explorer can be used as FTP client, you can try to type in ftp://ftp.usegalaxy.eu
but I would recommend you to follow the links above
Thielyfabian
@Thielyfabian
you will try thank you
Yusheng
@Yusheng_Tan_twitter
Hello there, I wonder how I can get permission to reuse a screenshot of Galaxy homepage in my thesis literature review section. Thanks!
Björn Grüning
@bgruening
@Yusheng_Tan_twitter afaik you do not need permissions. Use the screenshots as you like, as long as it contains your data and no data, or personal information from someone else
1 reply