BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2019-05-24T14:17:11-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/16Add "." to regex for Astrocyte file input2019-05-24T14:17:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd "." to regex for Astrocyte file input```
.*\.tar*
.*\.csv
```
not working```
.*\.tar*
.*\.csv
```
not workingv1.2.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/17Link changelog to index.md2019-05-24T14:17:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduLink changelog to index.mdv1.2.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/23Move untarBCL code into a bash script2019-05-24T14:16:58-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMove untarBCL code into a bash scriptmove the code from the process into 1 *or* 2 bash scripts in the ./workflow/scripts folder
either 1 script which tests for spaces and another one to run the untar... or 1 with both... @s189701, you decide...move the code from the process into 1 *or* 2 bash scripts in the ./workflow/scripts folder
either 1 script which tests for spaces and another one to run the untar... or 1 with both... @s189701, you decide...v1.2.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/21Remove spaces in input folders and files2019-05-24T14:16:57-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduRemove spaces in input folders and filesv1.2.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/25Add error checking for filename/folder names2019-05-24T14:16:03-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd error checking for filename/folder namesv1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/26Move module load into nextflow process2019-05-24T14:12:00-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMove module load into nextflow processsee cellranger_mkfastq for examplesee cellranger_mkfastq for examplev1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/tcga_shiny/-/issues/2remove legend from boxplots2019-05-24T12:51:39-05:00Spencer Barnesremove legend from boxplotsLegend is redundant. Should remove from plot.Legend is redundant. Should remove from plot.1.0.1Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/tcga_shiny/-/issues/1blank page on survival plot download2019-05-22T16:59:37-05:00Spencer Barnesblank page on survival plot downloadWhen downloading the survival plot, a blank page is printed into the pdf file before the plot.When downloading the survival plot, a blank page is printed into the pdf file before the plot.1.0.1Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/22Add error checking for filename/folder names2019-05-21T14:49:05-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd error checking for filename/folder namesv1.2.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/2Update test data2019-05-20T13:01:02-05:00Venkat MalladiUpdate test dataPossible datasets to include. Substitute some for mouse to test in each scenario.
Histone SE: https://www.encodeproject.org/experiments/ENCSR878KIY/
Histone PE: https://www.encodeproject.org/experiments/ENCSR203KEU/
Histone unreplica...Possible datasets to include. Substitute some for mouse to test in each scenario.
Histone SE: https://www.encodeproject.org/experiments/ENCSR878KIY/
Histone PE: https://www.encodeproject.org/experiments/ENCSR203KEU/
Histone unreplicated: https://www.encodeproject.org/experiments/ENCSR368ORV/
TF SE: https://www.encodeproject.org/experiments/ENCSR000DYI/
TF PE: https://www.encodeproject.org/experiments/ENCSR936XTK/
TF Unreplicated: https://www.encodeproject.org/experiments/ENCSR400WEK/
Currently:
TF PE (human): https://www.encodeproject.org/experiments/ENCSR729LGA/
Histone SE (mouse): https://www.encodeproject.org/experiments/ENCSR238SGC/Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/5Astrocyte documentation update2019-05-18T10:46:27-05:00Venkat MalladiAstrocyte documentation updateVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/54License spacing2019-05-17T13:51:10-05:00Venkat MalladiLicense spacingVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/53Add license2019-05-17T12:19:47-05:00Venkat MalladiAdd licenseAdd MIT license documentation to all parts of the codeAdd MIT license documentation to all parts of the codeVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/52Astrocyte Bug Fixes2019-05-16T09:10:45-05:00Venkat MalladiAstrocyte Bug Fixes- Fix generalized tests
- Links in astrocyte- Fix generalized tests
- Links in astrocyte1.0.4Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/4Remove Redundant Files2019-05-15T14:52:16-05:00Jonathan GesellRemove Redundant FilesRemove redundant yaml file.Remove redundant yaml file.Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/51Add in merge request template2019-05-15T13:19:11-05:00Venkat MalladiAdd in merge request templateVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/50Change Tests for Peak comparison to be greater than or equal to2019-05-15T10:02:03-05:00Venkat MalladiChange Tests for Peak comparison to be greater than or equal to1.0.4Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/48Single control fails at pool_and_psuedoreplicate2019-05-15T09:29:54-05:00Holly RuessSingle control fails at pool_and_psuedoreplicateThe pool_and_psuedoreplicate needs an update to use a single control sample. The current code doesn't workThe pool_and_psuedoreplicate needs an update to use a single control sample. The current code doesn't work1.0.4Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/46Fix Astrocyte links2019-05-15T09:28:20-05:00Holly RuessFix Astrocyte linksLinks from git (for instance design files examples) are not working in AstrocyteLinks from git (for instance design files examples) are not working in Astrocyte1.0.4Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/43failure to load python module-motif search2019-05-15T09:26:13-05:00Spencer Barnesfailure to load python module-motif searchMay-07 17:29:04.313 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'motifSearch (1)'Caused by:
Process `motifSearch (1)` terminated with an error exit status (1)Command executed: module load meme/4...May-07 17:29:04.313 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'motifSearch (1)'Caused by:
Process `motifSearch (1)` terminated with an error exit status (1)Command executed: module load meme/4.11.1-gcc-openmpi
module load bedtools/2.26.0
python3 /project/apps/astrocyte/data/runs/2200/2278/workflow/scripts/motif_search.py -d
design_annotatePeaks.tsv -g /project/shared/bicf_workflow_ref/GRCm38/genome.fa.txt -p
600Command exit status:
1Command output:
(empty)Command error:
Traceback (most recent call last):
File "/project/apps/astrocyte/data/runs/2200/2278/workflow/scripts/motif_search.py", line 11, in <module>
import pandas as pd
** ModuleNotFoundError: No module named 'pandas'**1.0.4Venkat MalladiVenkat Malladi