Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
  • Jan 31 2019 17:45
    bebatut opened #2270
  • Jan 31 2019 16:18
    cpreviti synchronize #2267
  • Jan 31 2019 14:15
    cpreviti synchronize #2267
  • Jan 31 2019 12:42
    bernt-matthias review_requested #2269
  • Jan 31 2019 12:42
    bernt-matthias edited #2269
  • Jan 31 2019 12:41
    bernt-matthias edited #2269
  • Jan 31 2019 12:40
    bernt-matthias synchronize #2269
  • Jan 31 2019 12:13
    cpreviti commented #2267
  • Jan 31 2019 12:07
    nsoranzo commented #2267
  • Jan 31 2019 12:01
    cpreviti synchronize #2267
  • Jan 31 2019 11:21
    cpreviti synchronize #2267
  • Jan 31 2019 09:47
    cpreviti synchronize #2267
  • Jan 31 2019 09:27
    cpreviti synchronize #2267
  • Jan 30 2019 20:38
    bernt-matthias commented #2131
  • Jan 30 2019 20:19
    hepcat72 commented #2239
  • Jan 30 2019 19:50
    lparsons commented #2239
  • Jan 30 2019 18:36
    bgruening commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2267
Shaimaa177
@Shaimaa177
How can I know the number of genes in a bed file and their locations? Which steps should I follow?
pvanheus
@pvanheus
is a Data Manager restricted to providing a single line for a data table at a time?
Marius van den Beek
@mvdbeek
No
A data manager can both create entries in multiple data tables (checkout the bowtie2 data manager for that). If you want to add multiple entries the produced data_manager.json should contain the additional entries.
{
  "data_tables": {
    "bowtie2_indexes": [
      {
        "dbkey": "phiX174",
        "name": "phiX174",
        "path": "phiX174",
        "value": "phiX174"
      }
    ],
    "tophat2_indexes": [
      {
        "dbkey": "phiX174",
        "name": "phiX174",
        "path": "phiX174",
        "value": "phiX174"
      }
    ]
  }
}
so here you’d add additional items in the inntermost array
for example
{
  "data_tables": {
    "bowtie2_indexes": [
      {
        "dbkey": "phiX174",
        "name": "phiX174",
        "path": "phiX174",
        "value": "phiX174"
      },
      {
        "dbkey": "phiX175",
        "name": "phiX175",
        "path": "phiX175",
        "value": "phiX175"
      },
    ],
  }
}
pvanheus
@pvanheus
ok then I must be doing something wrong, will look at the existing ones to see what. thanks!
pvanheus
@pvanheus
I recall that there is some trick to avoid having to do a client rebuild every time you run planemo serve - can someone remind me what it is please?
ah... --skip_client_build
pvanheus
@pvanheus
nope. that leaves me with a Galaxy with no UI. :(
pvanheus
@pvanheus
I thought that the Data Manager tool got passed the existing data table as an input... but testing shows that this is not true. It would be nice (for the pangoLEARN data manager) if this was true because it would allow skipping download of data we already have
pvanheusden
@pvanheusden:matrix.org
[m]
review & possible merge please: galaxyproject/tools-iuc#3617
abretaud
@abretaud:matrix.org
[m]
Looking into it
pvanheusden
@pvanheusden:matrix.org
[m]
are the filters that can be used with <options from_data_table...> documented somewhere?
pvanheusden
@pvanheusden:matrix.org
[m]
ah thanks. I see sort_by does not have an order attribute... pity... because I'd really like to specify descending order...
pvanheusden
@pvanheusden:matrix.org
[m]
I'll make a PR adding that capability...
M Bernt
@bernt-matthias
Yeah, that seems useful.
Jennifer Hillman-Jackson
@jennaj
Hi all -- Did I guess the answer right? Is a bit sparse and not exact, maybe someone can help add more details? It seems that they are not pulling the correct version of python into their environment. https://help.galaxyproject.org/t/conda-detected-but-not-work/5844 Thanks!
Anna Syme
@AnnaSyme
I was wondering if there were plans to wrap the unimap tool? This is now recommended for some types of alignments over minimap2 (as mentioned in the latest minimap2 release notes: https://github.com/lh3/minimap2/releases/tag/v2.18). Thanks if possible!
Björn Grüning
@bgruening
I created this issue here: galaxyproject/tools-iuc#3622
Anna Syme
@AnnaSyme
thanks @bgruening !
Francois STUDER
@studyfranco
Hello,
Francois STUDER
@studyfranco
I replied to @jennaj on https://help.galaxyproject.org/t/conda-detected-but-not-work/5844
I wanted know how you launch a job ? Do you use popen ?
Best regards
Marius van den Beek
@mvdbeek
@studyfranco Does your conda command (/opt/conda/bin/conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel iuc --channel defaults --channel R --name mulled-v1-5b73db27209dd7e83d26bd4dedeadbcf356c9297c08644dec23df66a734a236c python=2.7 scipy matplotlib Pillow reportlab tk ConfigParser) succeed on the command line ?
You may have combined incompatible versions, and then Conda can’t create the environment
Also please don’t set conda_exec
You also don’t want to set conda_auto_init
The conda_prefix must match your conda setup, so I guess that should be /opt/conda
pvanheusden
@pvanheusden:matrix.org
[m]
I'm writing a wrapper for nextclade which has a bunch of optional file inputs (e.g. --input-qc-config). If I make these visible as <param type="data" optional="true"> it seems they are assigned an input even if the chooser shows "Nothing selected". Is there a way to have optional dataset inputs without guarding each one in a <conditional> to activate / deactive it?
bgruening
@bgruening:matrix.org
[m]

If I make these visible as <param type="data" optional="true"> it seems they are assigned an input even if the chooser shows "Nothing selected".

This should be totally fine.

what do you mean with "are assigned an input"?
pvanheusden
@pvanheusden:matrix.org
[m]
Galaxy picks up the most recent dataset of the type of the input and assigns that...
Marius van den Beek
@mvdbeek
That doesn’t seem right
bgruening
@bgruening:matrix.org
[m]
that should not happen
pvanheusden
@pvanheusden:matrix.org
[m]
so for example input-qc-config is type JSON input... it picks up a JSON from the history and adds that to the command line
let me make a minimal example to share.
bgruening
@bgruening:matrix.org
[m]
can you paste in here the complete param please?
Francois STUDER
@studyfranco
@mvdbeek Yep, the command succeed when I do it manually. Galaxy detect this environment.
In fact, the command: . '/home/galaxy/.conda/bin/activate' '/home/galaxy/.conda/envs/mulled-v1-5b73db27209dd7e83d26bd4dedeadbcf356c9297c08644dec23df66a734a236c' > conda_activate.log 2>&1 work if I use it.
And when I launch the script command, it work fine too. This is why I am lost.
Marius van den Beek
@mvdbeek
Please fix the setup, this cannot work.
conda_prefix: /home/galaxy/.conda
conda_exec: /opt/conda/bin/conda (I have a symbolic link: ln -s /opt/conda/bin /home/galaxy/.conda/)
you should just set conda_prefix to /opt/conda/
Remove conda_exec too please
Francois STUDER
@studyfranco
I removed conda_exec set conda_prefix: /opt/conda and restart my galaxy server, I wait it now
Marius van den Beek
@mvdbeek
You’ll need to reinstall the environment too, you can do this from the admin panel -> admin -> manage tool dependencies
pvanheusden
@pvanheusden:matrix.org
[m]
and now... when I delete that section of the tool config and re-write it, the problems goes away. haha
Francois STUDER
@studyfranco
I have this output:
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
galaxy.tool_util.deps.resolvers.conda DEBUG 2021-04-23 11:21:17,362 [pN:main.web.1,p:1826,w:1,m:0,tN:uWSGIWorker1Core3] Removing failed conda install of [CondaTarget[python,version=2.7], CondaTarget[scipy,unversioned], CondaTarget[matplotlib,unversioned], CondaTarget[Pillow,unversioned], CondaTarget[reportlab,unversioned], CondaTarget[tk,unversioned], CondaTarget[ConfigParser,unversioned]]
galaxy.tool_util.deps.conda_util DEBUG 2021-04-23 11:21:17,363 [pN:main.web.1,p:1826,w:1,m:0,tN:uWSGIWorker1Core3] Executing command: /opt/conda/bin/conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel iuc --channel defaults --channel R --name __python@2.7 python=2.7
Collecting package metadata (current_repodata.json): ...working... galaxy.tool_util.deps DEBUG 2021-04-23 11:21:25,679 [pN:main.web.1,p:1826,w:1,m:0,tN:uWSGIWorker1Core2] Dependency python not found.
Marius van den Beek
@mvdbeek
Please provide versions for all dependencies
In your case scipy and matplotlib
Francois STUDER
@studyfranco
Sorry, I badly explain