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I am having a hard time running the pipeline with `caper` on SCG (SLURM). I am using the `conda` environment, which I just uninstalled and reinstalled according to the most recent update. I ran the fo…
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Hi!
I'm currently working on setting up snovault for use on the Google Cloud Platform. I am using a clean Ubuntu 16.04 VM (largely following the instructions on the README.md with linuxbrew).
I am a…
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The mass errors shown in issue #1 are incorrect (they are far too large). For example
```
# mono PPMErrorCharterPython.exe -I:/data/MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02.mzid -EValue:1E…
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**Incompatibility issues with custom reference genome**
Macs2 peak calling fails if the FASTA file used to build a custom genome database does not follow the `chr[\dXY]` naming convention. For ex…
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After installing all the python3 packages in the docker container...
```
wget https://github.com/PNNL-Comp-Mass-Spec/PPMErrorCharter/releases/download/v1.2.7190/PPMErrorCharterPython_Program.zip
…
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@alchemistmatt , would be possible to provide the InputFilePath as an argument option as well?
something like:
```
PeptideHitResultsProcRunner.exe -I:/data/file_whatever_.tsv -M:blahblah
```
…
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It looks like IDR peaks are being used to generate raw peak statistics. The peak statistics for the raw peaks and IDR peaks are identical in the HTML report, and the reported numbers of raw peaks and …
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The pipeline fails in the `call-filter` step:
```
INFO 2018-12-02 11:16:03 MarkDuplicates Reads are assumed to be ordered by: coordinate
#
# A fatal error has been detected by the Java R…
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**Describe the bug**
I got an error when I ran `conda/install_dependencies.sh` on SCG:
```
PaddingError: Placeholder of length '80' too short in package /labs/smontgom/nicolerg/MOTRPAC/PIPELINES/at…