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This command takes ages for a HiSeq/XTen run, and it only uses one core, so I think that we could detach it and continue to tarball the next run. So basically at a given point we would have just one r…
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Hi,
I just cloned the repository and typed `ant jar` as suggested in the README. It didn't build. Here is the error message:
```
lucass@milou2 share $ git clone https://github.com/rdpstaff/classifie…
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Uppmax har lagt in en ny version GNU plot (4.6.5) som Sisyphus inte verkar vara kompatibel med.
Smeds updated
10 years ago
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Testing Piper, alignments run ok but qualimap fails with the error shown below
```
/proj/a2009002/piper_resources/programs/qualimap_v1.0/qualimap --java-mem-size=64G bamqc -bam /apus/v1/a2010002_n…
vezzi updated
10 years ago
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When running:
```
WholeGenome.sh --xml_input pipelineSetup.xml
```
or, using the NGI_pipeline:
```
piper -S /proj/a2010002/software/piper_bin/qscripts/DNABestPracticeVariantCalling.scala --xml_i…
vezzi updated
10 years ago
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Alright I'm trying to use sthlm2UUSNP on the flowcellrun level, e.g. the format `sthlm2UUSNP -i {input_dir} -o {output_dir} -f {flowcell}` and it's failing. At first I thought this was a FileAlreadyEx…
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Hi,
Not sure this is a bug, but using the http protocol http://charon-dev.scilifelab.se will redirect to the correct Charon interface.
![screen shot 2014-06-25 at 09 45 14](https://cloud.githubuserc…
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This issue is linked to #3 and #2 but it adds also a new problem
This are the steps I followed to run piper:
```
##convert to SNPseq format —> this is not properly working refer to issue #3
sthlm2U…
vezzi updated
10 years ago
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It would be good if the pipeline setup xml format was more flexible in the sense that it's one could specify the exact location of the fastq-files. Probably the files should contain the full project, …
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I am trying to use sthlm2UUSNP to convert a NGI-S project into a NGI-U project as a first step to test piper.
This is the folder organisation of the project G.Grigelioniene_14_01 (P_name, Sample name,…
vezzi updated
10 years ago