📝 updates to account for v12 reload

Author: migbro

COLLABORATIONS/openTARGETS/README.md

@@ -35,7 +35,7 @@ To create the histologies file, recommended method is to:
     library("tidyr")
     ```
 
-1. Pull the OpenPedCan repo (warning, it's 12GB ): https://github.com/PediatricOpenTargets/OpenPedCan-analysis, or just download the script from `analyses/pedcbio-sample-name/pedcbio_sample_name_col.R`
+1. Pull the OpenPedCan repo (warning, it's 12GB ): https://github.com/d3b-center/OpenPedCan-analysis, or just download the script from `analyses/pedcbio-sample-name/pedcbio_sample_name_col.R`
 1. Export from D3b Warehouse the latest existing cBio IDs to use for population. Ensure that the output is csv double-quoted. Currently that can be obtained using the sql command:
     ```sql
 
@@ -73,7 +73,7 @@ To create the histologies file, recommended method is to:
 1. Get a blacklist from D3b Warehouse, exporting table `bix_workflows.cbio_hide_reasons
 
 ### Run as standalone
-1. Download from https://github.com/PediatricOpenTargets/OpenPedCan-analysis the `analyses/pedcbio-sample-name/pedcbio_sample_name_col.R` or run from repo if you have it
+1. Download from https://github.com/d3b-center/OpenPedCan-analysis the `analyses/pedcbio-sample-name/pedcbio_sample_name_col.R` or run from repo if you have it
 1. Run `Rscript --vanilla pedcbio_sample_name_col.R -i path-to-histolgies-file.tsv -n path-to-cbio-names.csv -b Methylation`
 OR
 ### Run in repo
@@ -89,7 +89,7 @@ Rscript COLLABORATIONS/openTARGETS/merge_rsem_rds.R --first_file gene-expression
 
 
 ### File Transformation
-It's recommended to put datasheets in a dir called `datasheets`, downloaded files in it's own dir (in v12 it's `GF_INPUTS`) and the rest of the processed outputs into it's own dir (`study_build` for v12) to keep things sane and also be able to leverage existing study build script in `scripts/organize_upload_packages.py`
+It's recommended to put datasheets in a dir called `datasheets`, downloaded files in it's own dir (in v12 it's `DOWNLOADED_INPUTS`) and the rest of the processed outputs into it's own dir (`study_build` for v12) to keep things sane and also be able to leverage existing study build script in `scripts/organize_upload_packages.py`
 #### 1. COLLABORATIONS/openTARGETS/clinical_to_datasheets.py
  ```
 usage: clinical_to_datasheets.py [-h] [-f HEAD] [-c CLIN] [-s CL_SUPP]
@@ -117,7 +117,7 @@ optional arguments:
  Outputs a `data_clinical_sample.txt` and `data_clinical_patient.txt` for the cBio package, and a `bs_id_sample_map.txt` mapping file to link BS IDs to gnerated cBioPortal IDs based on the rules for creating a proper somatic event using column `parent_aliquot_id`
 
 Example run:
-`python3 COLLABORATIONS/openTARGETS/clinical_to_datasheets.py -f COLLABORATIONS/openTARGETS/header_desc.tsv -c histologies-formatted-id-added.tsv -b cbio_hide_reasons.tsv 2> clin.errs`
+`python3 ~/tools/kf-cbioportal-etl/COLLABORATIONS/openTARGETS/clinical_to_datasheets.py -f ~/tools/kf-cbioportal-etl/COLLABORATIONS/openTARGETS/header_desc.tsv -c histologies-formatted-id-added.tsv -b cbio_hide_reasons.tsv 2> clin.errs`
 
 #### 2. COLLABORATIONS/openTARGETS/rename_filter_maf.py
 
@@ -140,10 +140,10 @@ optional arguments:
 ```
 _NOTE_ for v11 input, I ran the following command `zcat snv-dgd.maf.tsv.gz | perl -e '$skip = <>; $skip= <>; while(<>){print $_;}' | gzip -c >> snv-consensus-plus-hotspots.maf.tsv.gz` to add DGD data
 
-_NOTE_ for v12 input,I would have following command `python3 ~/tools/kf-cbioportal-etl/COLLABORATIONS/openTARGETS/add_dgd_maf_to_openpedcan.py -i /home/ubuntu/tools/kf-cbioportal-etl/COLLABORATIONS/openTARGETS/maf_openpedcan_v12_header.txt -c openpedcan_v12.maf -t ../bs_id_sample_map.txt -m ../GF_INPUTS/snv-dgd.maf.tsv.gz` to add DGD data, which is more robust - however, there are data issues with DGD, so it was left out
+_NOTE_ for v12 input,I would have following command `python3 ~/tools/kf-cbioportal-etl/COLLABORATIONS/openTARGETS/add_dgd_maf_to_openpedcan.py -i /home/ubuntu/tools/kf-cbioportal-etl/COLLABORATIONS/openTARGETS/maf_openpedcan_v12_header.txt -c openpedcan_v12.maf -t ../bs_id_sample_map.txt -m ../DOWNLOADED_INPUTS/snv-dgd.maf.tsv.gz` to add DGD data, which is more robust - however, there are data issues with DGD, so it was left out
 
 Example run:
-`python3 COLLABORATIONS/openTARGETS/rename_filter_maf.py -m bs_id_sample_map.txt -v snv-consensus-plus-hotspots.maf.tsv.gz -s 1 -n openpedcan_v12`
+`python3 ~/tools/kf-cbioportal-etl/COLLABORATIONS/openTARGETS/rename_filter_maf.py -m bs_id_sample_map.txt -v snv-consensus-plus-hotspots.maf.tsv.gz -s 1 -n openpedcan_v12`
 
 #### 3. COLLABORATIONS/openTARGETS/cnv_to_tables.py
 Convert cnv table to cBio format - genes as rows, samples as cols, one for absolute CN, another for GISTIC-style
@@ -163,7 +163,7 @@ optional arguments:
 ```
 
 Example run:
-`python3 COLLABORATIONS/openTARGETS/cnv_to_tables.py -m bs_id_sample_map.txt  -c consensus_wgs_plus_cnvkit_wxs.tsv.gz -s openpedcan_v11`
+`python3 ~/tools/kf-cbioportal-etl/COLLABORATIONS/openTARGETS/cnv_to_tables.py -m bs_id_sample_map.txt  -c consensus_wgs_plus_cnvkit_wxs.tsv.gz -s openpedcan_v12`
 
 #### 4. COLLABORATIONS/openTARGETS/rename_export_rsem.R
 Note, I merged the tcga into the main rds. I also needed an instance with _64GB ram_ in order to calc z scores. Update: Can also achieve by setting up 32GB swap space 
@@ -189,12 +189,12 @@ Options:
 		Show this help message and exit
 ```
 Example run:
-`Rscript COLLABORATIONS/openTARGETS/rename_export_rsem.R --rna_rds gene_tcga_expression_common_merge.rds --map_id bs_id_sample_map.txt --type openpedcan_v11 --computeZscore R 2> rna_convert.errs`
+`Rscript ~/tools/kf-cbioportal-etl/COLLABORATIONS/openTARGETS/rename_export_rsem.R --rna_rds gene_tcga_expression_common_merge.rds --map_id bs_id_sample_map.txt --type openpedcan_v12 --computeZscore C++ 2> rna_convert.errs`
 
 #### 5. scripts/convert_fusion_as_sv.py
 
 Before running, to leverage an existing fusion conversion, I first ran:
-`COLLABORATIONS/openTARGETS/reformat_cbio_sample_index.py -t bs_id_sample_map.txt -n openpedcan_v12 > fusion_sample_name_input.txt`
+`~/tools/kf-cbioportal-etl/COLLABORATIONS/openTARGETS/reformat_cbio_sample_index.py -t bs_id_sample_map.txt -n openpedcan_v12 > fusion_sample_name_input.txt`
 to reformat the sample name index.
 ```
 usage: convert_fusion_as_sv.py [-h] [-t TABLE] [-f FUSION_RESULTS] [-o OUT_DIR] -m MODE
@@ -229,7 +229,7 @@ optional arguments:
                         json config file with meta information; see REFS/case_meta_config.json example
 ```
 Example run:
-`python3 scripts/organize_upload_packages.py -o processed -c COLLABORATIONS/openTARGETS/openpedcan_v12_case_meta_config.json`
+`python3 scripts/organize_upload_packages.py -o processed -c ~/tools/kf-cbioportal-etl/COLLABORATIONS/openTARGETS/openpedcan_v12_case_meta_config.json`
 
 #### 7. COLLABORATIONS/openTARGETS/case_list_from_datasheet.py
 Last step before validation and upload
@@ -251,4 +251,4 @@ optional arguments:
 ```
 
 Example run:
-`python3 COLLABORATIONS/openTARGETS/case_list_from_datasheet.py -d data_clinical_sample.txt -s openpedcan_v12 -c GTEx -m 3`
+`python3 ~/tools/kf-cbioportal-etl/COLLABORATIONS/openTARGETS/case_list_from_datasheet.py -d data_clinical_sample.txt -s openpedcan_v12 -c GTEx -m 3`

COLLABORATIONS/openTARGETS/openpedcan_v12_case_meta_config.json

@@ -115,7 +115,7 @@
     },
     "study": {
         "_comment": "see https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#cancer-study for detailed specifics",
-        "description": "<a href=\"https://github.com/PediatricOpenTargets/OpenPedCan-analysis\">OpenPedCan</a> is a collaborative project between the National Cancer Institute and the Children's Hospital of Philadelphia as part of the NCI's Childhood Cancer Data Initiative. Here, we harmonize pan-cancer data using <a href=\"https://kidsfirstdrc.org/\">KidsFirst Data Resource Center</a> workflows and harness <a href=\"https://github.com/AlexsLemonade/OpenPBTA-analysis/\">OpenPBTA analytics</a> workflows to scale and add modules across pediatric cancer datasets. This data has been integrated into the pediatric open targets platform to assist in development and query of the FDA's Relevant Pediatric Molecular Targets List (PMTL) to identify new therapeutics for children with cancer. This is the v12 release of this effort, for v10 please see <a href=\"https://pedcbioportal.kidsfirstdrc.org/study/summary?id=ped_opentargets_2021\">OpenPedCan v10</a>. For study release details, please see <a href=\"https://tinyurl.com/55cxz9am\">Release Notes</a>",
+        "description": "<a href=\"https://github.com/d3b-center/OpenPedCan-analysis\">OpenPedCan</a> is a collaborative project between the National Cancer Institute and the Children's Hospital of Philadelphia as part of the NCI's Childhood Cancer Data Initiative. Here, we harmonize pan-cancer data using <a href=\"https://kidsfirstdrc.org\">KidsFirst Data Resource Center</a> workflows and harness <a href=\"https://github.com/AlexsLemonade/OpenPBTA-analysis\">OpenPBTA analytics</a> workflows to scale and add modules across pediatric cancer datasets. This data has been integrated into the pediatric open targets platform to assist in development and query of the FDA's Relevant Pediatric Molecular Targets List (PMTL) to identify new therapeutics for children with cancer. This is the v12 release of this effort underlying the <a href=\"https://moleculartargets.ccdi.cancer.gov\">NCI's molecular targets platform</a>. For study release details, please see <a href=\"https://tinyurl.com/55cxz9am\">Release Notes</a>",
         "groups": "PUBLIC",
         "cancer_study_identifier": "openpedcan_v12",
         "reference_genome": "hg38",