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Anything more?
If it's your
job_working_directory, you can clean it using tmpwatch like this:/usr/bin/tmpwatch -v --mtime --dirmtime 7d /pathtoyoudir
@gmauro:matrix.org Its "database/jobs_directory/000/" guess you meant this directory
adjust also
7d with your needs
5 replies
@mrtiba: Hi @mrtiba , could you share your history with me? I'll provide you my mail by DM.
hmm, it seems to work on some galaxies
Yes, use
Operations on multiple datasets (... misleading ...) and hide/unhide/delete/undelete to your liking, that works for datasets and collections
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.
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 ?
even so the same region file work correctly on bcftools
I am not able to use Galaxy
usegalaxy.org does not work for me
Thanks for reporting.
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?
<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>
<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 .
Brackets and other special characters are sanitised by default for security reasons.
Please look at sanatizer in Galaxy and add that
You might also want to look at the chemicaltoolbox that deals with smiles and molecules handling.
@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
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)