User: matthias.desmet

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Belgium
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7 months ago
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2 years, 9 months ago
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m**************@ugent.be

Posts by matthias.desmet

<prev • 54 results • page 1 of 6 • next >
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hg38 on galaxy rsync server/cvmfs
... Hi all, Is there any reference data available on the the Galaxy rsync/cvmfs server for hg38? I don't seem to be able to find the right path, and I'm wondering if I'm perhaps missing something. Thanks! M ...
cvmfs hg38 rsync written 7 months ago by matthias.desmet150 • updated 7 months ago by Jennifer Hillman Jackson25k
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Error uploading files - no data
... Hi, When trying to upload a local file through the interface to our local Galaxy instance I'm getting a `Failed: Bad Request (400)` error. The Galaxy log reports the following galaxy.tools DEBUG 2016-06-28 12:40:23,959 Validated and populated state for tool request (74.210 ms) galaxy.tools ...
upload written 2.1 years ago by matthias.desmet150 • updated 2.1 years ago by Jennifer Hillman Jackson25k
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using conda env instead of venv in job_conf.xml
... Hi, We've recently switched our galaxy server form virtualenv to conda. In the previous setup we used the galaxy venv in the job configuration. Is it possible to to the same for a conda environment? How do we need to set this up? Thanks Matthias ...
cluster galaxy conda written 2.3 years ago by matthias.desmet150
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Galaxy release 16.04 - timeframe
... Hi, Anyone have any idea when the next version of Galaxy will be released? The projected date was 04/25 as far is I know. Thanks! M ...
16.04 release written 2.3 years ago by matthias.desmet150 • updated 2.3 years ago by Martin Čech ♦♦ 4.8k
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Answer: A: Galaxy sourcing reference data from location not in data table
... Found it, Apparently galaxy also sources loc files from the installation directory of any data managers you might have (had) installed. In my case, I used to have data_manager_fetch_genome_all_fasta and used it to download the hg19 genome. Then we switched to manual editing of the loc files and do ...
written 2.3 years ago by matthias.desmet150
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Answer: A: Cannot start local Galaxy after upgrade to v16.01
... Try running the "common_startup.sh" script in the scripts folder (/opt/galaxy/scripts/common_startup.sh) before you restart. This way all required dependencies will be installed using the custom galaxy pip version. Also, you might want to consider upgrading your python version, as 2.6 is nearing de ...
written 2.3 years ago by matthias.desmet150
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Galaxy sourcing reference data from location not in data table
... Hi all, I'm having a issue with the picard tools downloaded from the toolshed. When trying to use the CollectInsertSizeMetrics tool in the picard suite, I'm asked to use a reference genome as input. This is no problem, since the tool should read the available references from the all_fasta.loc file. ...
picard data_tables written 2.3 years ago by matthias.desmet150
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Comment: C: Disable user creation through interface
... Hi, thanks for the answer. This appears to be kind of a stupid question, I should have looked through the config file first. My bad! M ...
written 2.4 years ago by matthias.desmet150
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Disable user creation through interface
... Hi, Does anyone know how I could disable the interface option to register as a new user? We'd like our local instance to only be accessible by users registered in our LDAP, so a user shouldn't be able to create an account on its own. Thanks! M ...
users admin written 2.4 years ago by matthias.desmet150 • updated 2.4 years ago by Hotz, Hans-Rudolf1.8k
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Answer: A: Error running Picard tools (devteam)
... The answer given by Jennifer does help with the SAM validation error,  However, this error is ignorable. The main issue was there was something wrong with the tmp directory used by the java runtime. Clearing the tmp directory cleared the issue.   ...
written 2.5 years ago by matthias.desmet150

Latest awards to matthias.desmet

Popular Question 20 months ago, created a question with more than 1,000 views. For Uncaught exception in exposed API method when creating data library (new interface)
Popular Question 20 months ago, created a question with more than 1,000 views. For Error running Picard tools (devteam)
Scholar 2.3 years ago, created an answer that has been accepted. For A: Uncaught exception in exposed API method when creating data library (new interfa
Scholar 2.5 years ago, created an answer that has been accepted. For A: Uncaught exception in exposed API method when creating data library (new interfa
Scholar 2.5 years ago, created an answer that has been accepted. For A: Uncaught exception in exposed API method when creating data library (new interfa
Scholar 2.5 years ago, created an answer that has been accepted. For A: Uncaught exception in exposed API method when creating data library (new interfa
Scholar 2.7 years ago, created an answer that has been accepted. For A: Uncaught exception in exposed API method when creating data library (new interfa

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