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[unknown]
DESeq2 or EdgeR or Limma without replication [usegalaxy.org support] error
Hello, I am trying to do different expression using DESeq2, or EdgeR, or Limma but it always obtain error.
Can I use these tool without rep…
esearch -db nuccore -query "biomol_rRNA[prop]" | efetch -format fasta? I would like a reference that contains all known rRNAs to use in a QC step for RNA-Seq data. I looked at the existing ncbi fetch data manager tools and they don't appear to support this type of query.
$output.files_path points to wrong directory is there a fix? [Uncategorized] tool-dev
Many of my Qiime2 tools are failing in Galaxy because the wrapper outputs additional html files to $output.files_path, however ‘files_path’ …
[unknown]
computeMatrix Deeptools [usegalaxy.org support] admin, workflow
How long does it take to complete a job for computeMatrix from Deeptools.
I am not able to get anything even after a day.
@nsoranzo Thanks, so my goal is to output an index.html file so the full command is :
qiime demux summarize --i-data=$idata
if str($pn):
--p-n=$pn
end if
--o-visualization=output.qzv
;
qiime tools export --input-path output.qzv --output-path out
&& mkdir -p '$output.files_path'
&& cp -r out/* '$output.files_path'
&& mv '$output.files_path/index.html' '$output'
The logs show :
qiime demux summarize --i-data=/home/manager/galaxy/database/files/002/dataset_2034.dat --p-n=10000 --o-visualization=output.qzv ; qiime tools export --input-path output.qzv --output-path out && mkdir -p '/home/manager/galaxy/database/jobs_directory/001/1918/dataset_2098_files' && cp -r out/* '/home/manager/galaxy/database/jobs_directory/001/1918/dataset_2098_files' && mv '/home/manager/galaxy/database/jobs_directory/001/1918/dataset_2098_files/index.html' '/home/manager/galaxy/database/files/002/dataset_2098.dat'
As you can see the issue is that im getting an error for creating the directory because it is read-only. I just need to get the index.html and its accompanying files in the same output directory.
ps: I apologize if my post is a bit long or if im asking in the wrong place as im new to Galaxy .
Galaxy migration from sqlite to postgres almost worked [Uncategorized]
Good Day. This is my first post and I’m completely new to Galaxy (2 weeks) so please be gentle. I’ve been given the task to migrate a mult…
custom data source tool error [Uncategorized] tool-dev
I’m trying to create a custom data source tool that links to our site and when a button is pressed it returns a csv to Galaxy, however I got…
--- qiime_demux_summarize.xml 2020-01-15 23:58:08.167977529 +0000
+++ qiime_demux_summarize.xml.new 2020-01-15 23:46:40.220604152 +0000
@@ -1,28 +1,33 @@
<?xml version="1.0" ?>
-<tool id="qiime_demux_summarize" name="qiime demux summarize">
+<tool id="qiime_demux_summarize" name="qiime demux summarize" version="1.0">
<description> - Summarize counts per sample.</description>
<requirements>
<container type="docker">qiime2/core</container>
</requirements>
<command ><![CDATA[
-qiime demux summarize --i-data=$idata
+qiime demux summarize --i-data='$idata'
#if str($pn):
--p-n=$pn
#end if
--o-visualization=output.qzv
-;
-qiime tools export --input-path output.qzv --output-path out
-&& mkdir -p '$output.files_path'
-&& cp -r out/* '$output.files_path'
-&& mv '$output.files_path/index.html' '$output'
+&& qiime tools export --input-path output.qzv --output-path out
+&& mkdir -p '$output.extra_files_path'
+&& cp -r out/* '$output.extra_files_path'
+&& mv '$output.extra_files_path/index.html' '$output'
]]></command>
<inputs>
<param format="qza,no_unzip.zip" label="--i-data: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be summarized. [required]" name="idata" optional="False" type="data"/>TRINITY run time [Uncategorized]
I am trying to assembled data using TRINITY. It has been well over 24hrs and it still shows that the analysis job is still running. Is that …
RNA-STAR has been queued [Uncategorized]
I’m rather new to Galaxy. I’m trying to run RNA-STAR using mapped.bam file, The job has been queued now for more than 24 hrs. Is this norma…
[unknown]
New Galaxy account [Uncategorized]
Hello,
Please I would like to ask if it is okay and allowed to create another account on Galaxy because I used almost all the available spa…
[unknown]
Trim Galore latest version update on usegalaxy.eu? [Uncategorized]
Hello,
I am wondering whether it would be possible to update the ‘Trim Galore’ to the latest version. It would be appreciated in advance.
R…
@nsoranzo Thanks again for trying to help as I've been stuck on it for a while now. I'm testing just by using the Galaxy UI uploading a .qza file and using that as input for the tool. I have changed my script to mirror yours by changing from files_path to extra_files_path.
The command:
galaxy.jobs.command_factory INFO 2020-01-16 11:38:44,838 [p:30062,w:1,m:0] [LocalRunner.work_thread-1] Built script [/home/manager/galaxy/database/jobs_directory/001/1939/tool_script.sh] for tool command
[qiime demux summarize --i-data='/home/manager/galaxy/database/files/002/dataset_2116.dat' --p-n=10000 --o-visualization=output ;
qiime tools export --input-path output.qzv --output-path out
&& mkdir -p '/home/manager/galaxy/database/jobs_directory/001/1939/dataset_2119_files'
&& cp -r out/* '/home/manager/galaxy/database/jobs_directory/001/1939/dataset_2119_files'
&& mv '/home/manager/galaxy/database/jobs_directory/001/1939/dataset_2119_files/index.html' '/home/manager/galaxy/database/files/002/dataset_2119.dat']
galaxy.jobs.runners DEBUG 2020-01-16 11:38:44,876 [p:30062,w:1,m:0] [LocalRunner.work_thread-1] (1939) command is: rm -rf working;
mkdir -p working;
cd working;
docker inspect qiime2/core > /dev/null 2>&1
[ $? -ne 0 ] && docker pull qiime2/core > /dev/null 2>&1
docker run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -v /home/manager/galaxy:/home/manager/galaxy:ro -v /home/manager/galaxy/tools/qiime2:/home/manager/galaxy/tools/qiime2:ro -v /home/manager/galaxy/database/jobs_directory/001/1939:/home/manager/galaxy/database/jobs_directory/001/1939:ro -v /home/manager/galaxy/database/jobs_directory/001/1939/working:/home/manager/galaxy/database/jobs_directory/001/1939/working:rw -v /home/manager/galaxy/database/files:/home/manager/galaxy/database/files:rw -w /home/manager/galaxy/database/jobs_directory/001/1939/working --net none --rm --user 1000:1000 qiime2/core /home/manager/galaxy/database/jobs_directory/001/1939/tool_script.sh > ../tool_stdout 2> ../tool_stderr; return_code=$?; cd '/home/manager/galaxy/database/jobs_directory/001/1939';
[ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True
python "metadata/set.py"; sh -c "exit $return_code"The error:
execution finished: /home/manager/galaxy/database/jobs_directory/001/1939/galaxy_1939.sh
galaxy.jobs.output_checker DEBUG 2020-01-16 11:39:08,271 [p:30062,w:1,m:0] [LocalRunner.work_thread-1]
job failed, detected state generic_error, standard error is -
[mkdir: cannot create directory
‘/home/manager/galaxy/database/jobs_directory/001/1939/dataset_2119_files’: Read-only file system
]
galaxy.jobs DEBUG 2020-01-16 11:39:08,320 [p:30062,w:1,m:0] [LocalRunner.work_thread-1] (1939) setting dataset 2119 state to ERROR
galaxy.jobs INFO 2020-01-16 11:39:08,405 [p:30062,w:1,m:0] [LocalRunner.work_thread-1] Collecting metrics for Job 1939 in /home/manager/galaxy/database/jobs_directory/001/1939
galaxy.jobs DEBUG 2020-01-16 11:39:08,414 [p:30062,w:1,m:0] [LocalRunner.work_thread-1] job 1939 ended (finish() executed in (138.691 ms))
galaxy.tools.error_reports DEBUG 2020-01-16 11:39:08,423 [p:30062,w:1,m:0] [LocalRunner.work_thread-1] Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7f91e30937d0> generated response NoneI'm assuming the error is referring to the mkdir command, so possibly the extra_files_path is pointing to the wrong directory for me.
mkdir -p '/tmp/tmpyasl800v/job_working_directory/000/2/working/dataset_ab8002bd-f6c1-4b38-a1d3-dd56b4ce6f7f_files' , where the main difference is that in your case the working subdirectory is missing. What Galaxy version are you using?
Select first line from datastes (Text manipulation) [Uncategorized]
Hi everyone I would like to ask you the opinion that can help me to overcome the little problem that I am facing. Once I use Select first li…
