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Please describe needed access to the best of your ability:
First name: Andreas
Last name: Rauscheker
Google Email: `andreas.rauschecker@gmail.com `
Collaborator Emails: Andreas has a collabora…
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Reference files that I found in the code:
```
## scripts/Align_fastq.sh
BWA_INDEX=${LG3_HOME}/resources/bwa_indices/hg19.bwa
## runs_demo/_run_Recal
ILIST=${ILIST:-${LG3_HOME}/resources/SeqCap_…
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Going to use this thread to scribble down when I discover other hardcoded paths to reference files but also to scripts (as the below example also includes):
```sh
$ head -10 FilterMutations/mutati…
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Example:
```r
curl --netrc -T file ftps://ftp.box.com/box_location
```
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Hi, I want to use this tool to get some protein in-silico digest sequence and m/z value with kinds of modification.
I think the pepindex file might contain such infomation, but is not human readab…
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Semi-randomly, some scripts call `python` on the PATH;
```sh
$ grep -E "^(|.* )python " scripts/*.sh
scripts/annotate_mutations_from_bam.sh:python "${LG3_HOME}/scripts/annotate_mutations_from_bam…
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@chris-mcginnis-ucsf I recently applied DoubletFinder to my single nuclei data, which is whole tumor sample preparation. I run DoubletFinder on individual sample and here I show one example where ther…
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So, I forgot that we have a `qsub` tool on C4 that emulates Torque/PBS `qsub`. However, it does _not_ support CLI option `-d ` which set the working directory. The LG3 Pipeline uses it solely(*) as …
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Add queue status page for Slurm similarly to SGE.
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Moving from sysadm issue.