User: matthias.desmet

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Posts by matthias.desmet

<prev • 53 results • page 1 of 6 • next >
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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 17 months ago by matthias.desmet130 • updated 17 months ago by Jennifer Hillman Jackson23k
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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 19 months ago by matthias.desmet130
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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 19 months ago by matthias.desmet130 • updated 19 months ago by Martin Čech ♦♦ 4.2k
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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 20 months ago by matthias.desmet130
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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 20 months ago by matthias.desmet130
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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 20 months ago by matthias.desmet130
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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 21 months ago by matthias.desmet130
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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 21 months ago by matthias.desmet130 • updated 21 months ago by Hotz, Hans-Rudolf1.7k
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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 21 months ago by matthias.desmet130
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Error running Picard tools (devteam)
... Hi all, After debugging the install of picard, I'm testing it out. When running the MarkDuplicates tool I get the following error:  Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m Ignoring SAM validation error: ERROR: Record 1, Read name D74F8:06451:05495, RG ID on SAMRec ...
picard written 21 months ago by matthias.desmet130

Latest awards to matthias.desmet

Scholar 20 months ago, created an answer that has been accepted. For A: Uncaught exception in exposed API method when creating data library (new interfa
Scholar 21 months ago, created an answer that has been accepted. For A: Uncaught exception in exposed API method when creating data library (new interfa
Scholar 21 months ago, created an answer that has been accepted. For A: Uncaught exception in exposed API method when creating data library (new interfa
Scholar 22 months ago, created an answer that has been accepted. For A: Uncaught exception in exposed API method when creating data library (new interfa
Scholar 24 months 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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