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Björn Grüning
@bgruening
Can you sent an error report?
Hawke996
@Hawke996
I have but they can't figure out the problem either
Jeevan Karloss
@ajkarloss
We have a test Galaxy instance and the "database/jobs_directory" occupies lots space. I am planning to delete it folders inside. I am not sure about consequences of that. Could you someone tell me the consequences? I guess the history will be gone
Anything more?
Nicola Soranzo
@nsoranzo:matrix.org
[m]
Histories won't be affected
Jeevan Karloss
@ajkarloss
@nsoranzo:matrix.org Thanks. Anything else?
gmauro
@gmauro:matrix.org
[m]
If it's your job_working_directory, you can clean it using tmpwatch like this:
/usr/bin/tmpwatch -v --mtime --dirmtime 7d /pathtoyoudir
Jeevan Karloss
@ajkarloss
@gmauro:matrix.org Ok, Thanks a lot
@gmauro:matrix.org Its "database/jobs_directory/000/" guess you meant this directory
gmauro
@gmauro:matrix.org
[m]
you need to use the full path
adjust also 7d with your needs
Jeevan Karloss
@ajkarloss
Thanks
Jeevan Karloss
@ajkarloss
@gmauro:matrix.org Just to make sure: So, these folders are created while running job and not needed further and it wont affect histories. Am I correct?
Gianmauro Cuccuru
@gmauro
correct
Jeevan Karloss
@ajkarloss
Thanks a lot
Matt Chambers
@chambm
Is there a way to change the datatype of all datasets in a collection?
5 replies
mrtiba
@mrtiba
Hi. I'm trying to make a hybrid montage using the unicycler and when I upload the reads they show up as unavailable. They are in fastq format. Can anyone help me?
Thanks
2 replies
Cristóbal Gallardo
@gallardoalba:matrix.org
[m]
@mrtiba: Hi @mrtiba , could you share your history with me? I'll provide you my mail by DM.
martenson
@martenson:matrix.org
[m]
can you hide a collection in history?
hmm, it seems to work on some galaxies
Marius
@mvdbeek:matrix.org
[m]
Yes, use Operations on multiple datasets (... misleading ...) and hide/unhide/delete/undelete to your liking, that works for datasets and collections
martenson
@martenson:matrix.org
[m]
My use case was to actually make a hidden collection as an output of a tool. That one I do not seem to be able to work out.
Marius
@mvdbeek:matrix.org
[m]
Yeah, that's not supported
If the collection is not useful most of the time you could make it conditional, but hidden collections (or hidden datasets that are not part of a collection) are probably not great for users ?
Serekh
@Serekh2_twitter
why does samtools mpileup -I flag which is a position region file doesn't work and gives error [E::mpileup] fail to parse region '' with 0
even so the same region file work correctly on bcftools
lightsaber53
@lightsaber53
Hi, why is the galaxy server down?
I am not able to use Galaxy
bgruening
@bgruening:matrix.org
[m]
Which one there are more than 200 :-)
lightsaber53
@lightsaber53
The main server
usegalaxy.org does not work for me
bgruening
@bgruening:matrix.org
[m]
Yes I can confirm and will ping the admins.
Thanks for reporting.
Jiaqi
@ZeroDesigner
Screen Shot 2021-06-20 at 10.20.33 PM.png
Hi,I am trying to create a tool for galaxy.And the problem is the input value is right and the value in the command line is not same with the input value ? How can I fix it?
bgruening
@bgruening:matrix.org
[m]
Can you share this tool and the command line you expect?
Jiaqi
@ZeroDesigner
yeah
<tool id="aidd_1" name="REIVENT" version="0.1.0">
<requirements>
<requirement type="package" version="1.0.1"> REIVENT </requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
docker run luskyqi/acaflow2galaxy:reivent_latest /root/miniconda3/envs/REINVENT/bin/python /home/REINVENT/main.py --scoring-function tanimoto --scoring-function-kwargs query_structure ${input} --num-steps $step > $log
]]></command>

<inputs>
<param type="text" name="input" help="The Molecule's SMILES string" label="Input SMILES" value="OC1=CC=CC(C(N[C@@H](CSC2=CC=CC=C2)[C@H](O)CN3C[C@](CCCC4)([H])[C@]4([H])C[C@H]3C(N[C@H](C([H])O)CC5C(NCC5)=O)=O)=O)=C1C"/>
<param type="integer" name="step" help="The Steps Applied" label="Stpes Num" value = "100" />
</inputs>
<outputs>
<data name="log" format="txt" />
</outputs>
<citations>
<citation>https://arxiv.org/abs/1704.07555</citation>
</citations>
</tool>
This is my command line . As for the environment , I have not learned how to upload its requirement package .
bgruening
@bgruening:matrix.org
[m]
Brackets and other special characters are sanitised by default for security reasons.
Please look at sanatizer in Galaxy and add that
Jiaqi
@ZeroDesigner

Brackets and other special characters are sanitised by default for security reasons.

Thank you

bgruening
@bgruening:matrix.org
[m]
You might also want to look at the chemicaltoolbox that deals with smiles and molecules handling.
Jiaqi
@ZeroDesigner

Yes , I am following your github account.

You might also want to look at the chemicaltoolbox that deals with smiles and molecules handling.

bgruening
@bgruening:matrix.org
[m]
@ZeroDesigner can you tool deal with multiple smiles at ones? Then I would recommend to take the smile input as file and not as string
Björn Grüning
@bgruening
@lightsaber53 please try again!
Jiaqi
@ZeroDesigner

@ZeroDesigner can you tool deal with multiple smiles at ones? Then I would recommend to take the smile input as file and not as string

I have thought it which deals with multiple smiles at ones. But for user , I think it would be better to deal handle one sentence each time.

bgruening
@bgruening:matrix.org
[m]
If you use files you don't need to worry about the encoding and the user could potentially input moledules in different formats (and convert them esily to smiles for your tool)
Jiaqi
@ZeroDesigner
Yes, I will take it. @bgruening:matrix.org