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James Taylor
@jxtx
@sadvani6 Are you using trimmomatic with paired inputs, and only trying to align the paired outputs? bwa is unhappy because you are giving it two files with different numbers of reads -- can't be proper paired ends.
galaxybot
@galaxybot

[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…

Robert Leach
@hepcat72
Is there a data manager that could essentially do the following to create a reference from ncbi: 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.
FYI, I've never used a data manager before. This is my first shot. I watched a presentation from the docs on adding references and read through some forum posts.
galaxybot
@galaxybot
[unknown]
$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’ …
Patamarerk
@Patamarerk
Hi all, my disk status in cloudman console is full (320/320G) but in my Analyze data page it is just 200 GB. I have purge deleted my old data but it doesn't free more space in the console. How can I free more space? Please help. Thank you very much.
Valid95
@Valid95
Hi everyone, I would like to ask a question about the extraction and annotation of differentially expressed genes procedure. I would like to run Filter data on any column using simple expressions on Galaxy and put the DEseq2 result file but I cannot find my DEseq2 result file while as an input file in the filter box, it doesn't show that file but shows other files. How can I solve that issue? Thank you very much in advance.
galaxybot
@galaxybot

[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.

Valid95
@Valid95
I have a question related to the normalization of counts. When I run DEseq2 I got lots of zero in my normalized count table. Do you know how can I properly normalize reads and look at if my samples are significantly different compared to the genes?
Gabriel Benavidez
@gabrielbenavidez
@jxtx Thank you for your help. In my case $output.files_path is pointing to 'database/job_directory/###/datasetId/dataset_Id_files' but $output goes to 'files/###/datasetId.dat'. I was wondering about this ### number and how that changes. For me it was 000 then it went to 001 now its at 002. So every job I run is in the 002 directory. So my concern is why does this number keep changing when it's different than the dataset Id?
Nicola Soranzo
@nsoranzo
@gabrielbenavidez That's how Galaxy organises the datasets to not put all the files in the same directory, you really shouldn't rely on any particular naming scheme.
Gabriel Benavidez
@gabrielbenavidez

@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 .

Nicola Soranzo
@nsoranzo
@gabrielbenavidez Can you try replacing $output.files_path with $output.extra_files_path ?
Gabriel Benavidez
@gabrielbenavidez
@nsoranzo it's giving me the same directory not sure why.
Nicola Soranzo
@nsoranzo
@gabrielbenavidez If you can share the full tool XML, e.g. on https://gist.github.com/ , it may be easier to find the issue
Gabriel Benavidez
@gabrielbenavidez
galaxybot
@galaxybot
[unknown]
Galaxy migration from sqlite to postgres almost worked [Uncategorized]
Good Day. This is my first post and I’m completely new to Galaxy (2 weeks) so please be gentle. I’ve been given the task to migrate a mult…
galaxybot
@galaxybot
[unknown]
custom data source tool error [Uncategorized] tool-dev
I’m trying to create a custom data source tool that links to our site and when a button is pressed it returns a csv to Galaxy, however I got…
Nicola Soranzo
@nsoranzo
@gabrielbenavidez I don't see anything specifically wrong in your tool, it works fine when tested with planemo. I only made the following changes and added a test:
--- qiime_demux_summarize.xml    2020-01-15 23:58:08.167977529 +0000
+++ qiime_demux_summarize.xml.new    2020-01-15 23:46:40.220604152 +0000
@@ -1,28 +1,33 @@
 <?xml version="1.0" ?>
-<tool id="qiime_demux_summarize" name="qiime demux summarize">
+<tool id="qiime_demux_summarize" name="qiime demux summarize" version="1.0">
     <description> - Summarize counts per sample.</description>
     <requirements>
         <container type="docker">qiime2/core</container>
     </requirements>
     <command ><![CDATA[
-qiime demux summarize --i-data=$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"/>
If you can share how you are testing the tool and the full error you are seeing.
galaxybot
@galaxybot
[unknown]
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 …
[unknown]
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…
BlizeGit
@BlizeGit
when I run "sh run.sh", it shows this error: ERROR: Invalid requirement: u'lib/galaxy/dependencies/pinned-requirements.txt' (from line 1 of requirements.txt)
does anyone know what is the cause
Nicola Soranzo
@nsoranzo
@BlizeGit Is that under which operating system? Windows?
galaxybot
@galaxybot

[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…

galaxybot
@galaxybot

[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…

galaxybot
@galaxybot
[nekrut] @Marius van den Beek: it is still impossible to run multiqc on fastqc output ifg fastqc was run on a paired collection. Are you aware of any efforts to address that?
Gabriel Benavidez
@gabrielbenavidez

@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 None

I'm assuming the error is referring to the mkdir command, so possibly the extra_files_path is pointing to the wrong directory for me.

Nicola Soranzo
@nsoranzo
@gabrielbenavidez This is weird, in my case it is 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?
I'm using planemo with an updated release_19.09
Gabriel Benavidez
@gabrielbenavidez
@nsoranzo Thats strange, I am using Galaxy version 19.05. Is this something updating my Galaxy instance might help with?
Gabriel Benavidez
@gabrielbenavidez
@nsoranzo Also I forgot to mention I am running the Qiime2 tools via a Docker container. Not sure if that has anything to do with the Read-only file system error.
Nicola Soranzo
@nsoranzo
@gabrielbenavidez I've noticed, in fact I'm running the tests with planemo test --biocontainers . I can confirm that I see the mkdir issue using release_19.05 , so updating to 19.09 will solve the problem.
Gabriel Benavidez
@gabrielbenavidez
@nsoranzo Thank you I will try updating now then.
galaxybot
@galaxybot
[unknown]
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…
Ayushi Jain
@ayushi.med_gitlab
Hi, I would want to know about the q value and its level and cutt-off for significance? Why is all my data being not significant based on the q value, even if p-value is significant?
The q-value provides a correction for the fact that you are performing many tests. The p-value is only valid for a single test. As far as a cut-off, the q-value is the lowest false discovery rate at which the test would be significant. So, you choose the cut off based on how many false positives you are willing to accept. e.g. if you choose q ≤ .05 as your cutoff, 5% of your positives are actually false discoveries (on average).
Ayushi Jain
@ayushi.med_gitlab
So when we run CuffDiff on the galaxy server, by default it takes p-value as <0.05 and q-value as <0.05 for the cut-offs. Is there any way that we could change those cut-offs and run our pipeline again?
Nadia Goué
@nagoue
Hi, I got an error using Trim Galore through Bismark last revision. (No problem if I run Trim Galore on it's own) . The problem is that the bismark option --temp_dir is set to /tmp/tmpxxxxx and not to galaxy temp dir (i.e. database). I guess something is wrong in bismark_wrapper.xml or .py ? May someone help ? maybe @bgruening ?
Björn Grüning
@bgruening
@nagoue is this happening on your instance or somewhere else?
Nadia Goué
@nagoue
on my instance 19.09
Björn Grüning
@bgruening
@nagoue bismark needs a lot of temporary space, because it creates several copies of the fastq (and ref-data)
To we have provided this tool a special temp location
try setting '$TEMP' in your job destination setting to a large storage that is available on all cluster nodes
Nadia Goué
@nagoue
I can't do that it depends on cluster configuration, I don't have hand on it.
Björn Grüning
@bgruening
mh, this is a pure Galaxy config, given you have some share-free space on the cluster
Nadia Goué
@nagoue
which is not on /tmp :(
Nadia Goué
@nagoue
ok so sorry I didn't catch it . What do you mean by job destination setting ? which config file do you refer to ?