Merge pull request #336 from mskcc/upgraded_facets

Upgraded_facets

.gitignore

@@ -46,3 +46,4 @@ roslin-build-log
 *.sif
 checksum.dat
 setup/examples/roslin_workflows_test.py
+config.variant.yaml

build/containers/facets/1.6.2/Dockerfile → build/containers/facets/1.6.3/Dockerfile

@@ -2,16 +2,16 @@ FROM alpine:3.8
 
 LABEL maintainer="Nikhil Kumar (kumarn1@mskcc.org)" \
       version.image="1.0.0" \
-      version.facets_suite="1.6.2" \
+      version.facets_suite="1.6.3" \
       version.facets="0.5.14"\
       version.alpine="3.8" \
       version.r="3.5.1" \
       version.pctGCdata="0.2.0" \
-      source.facets_suite="https://github.com/mskcc/facets-suite/releases/tag/1.6.2" \
+      source.facets_suite="https://github.com/mskcc/facets-suite/releases/tag/1.6.3" \
       source.facets="https://github.com/mskcc/facets/archive/v0.5.14.tar.gz"\
       source.r="https://pkgs.alpinelinux.org/package/edge/community/x86/R"
 
-ENV FACETS_SUITE_VERSION 1.6.2
+ENV FACETS_SUITE_VERSION 1.6.3
 ENV FACETS_VERSION 0.5.14
 ENV PCTGCDATA 0.2.0
 
@@ -26,7 +26,10 @@ RUN apk add --update \
     # for compilation
         && apk add build-base musl-dev python py-pip python-dev \
     # install cairo and R package system dependencies
-        && apk add cairo cairo-dev libxt-dev libxml2-dev font-xfree86-type1 \
+        && apk add cairo cairo-dev libxt-dev libxml2-dev font-xfree86-type1 msttcorefonts-installer \
+        # configure the installed fonts
+        && update-ms-fonts \
+        && fc-cache -f \
     # download and install R
         && apk add R R-dev \
     # download and unzip facets, facets-suite, pctGCdata
@@ -62,20 +65,6 @@ RUN apk add --update \
                 && sed -i "s/opt\/common\/CentOS_6-dev\/R\/R-3.1.3\//usr\//g" *.R \
                 && sed -i "s/opt\/common\/CentOS_6-dev\/python\/python-2.7.10\/bin\/python/usr\/bin\/env python/g" facets \
                 && sed -i "s/opt\/common\/CentOS_6-dev\/bin\/current\/python/usr\/bin\/env python/g" summarize_project.py \
-                #&& sed -i "s/IMPACT468_targets <-/# IMPACT468_targets <-/g" geneLevel.R \
-                #&& sed -i "s/msk_impact_468 <-/# msk_impact_468 <-/g" geneLevel.R \
-                #&& sed -i "s/setnames(IMPACT468_targets/# setnames(IMPACT468_targets/g" geneLevel.R \
-                #&& sed -i "s/IMPACT410_targets =/# IMPACT410_targets =/g" geneLevel.R \
-                #&& sed -i "s/setkey(IMPACT468_targets/# setkey(IMPACT468_targets/g" geneLevel.R \
-                #&& sed -i "s/IMPACT410_targets <-/# IMPACT410_targets <-/g" geneLevel.R \
-                #&& sed -i "s/msk_impact_410 <-/# msk_impact_410 <-/g" geneLevel.R \
-                #&& sed -i "s/setnames(IMPACT410_targets/# setnames(IMPACT410_targets/g" geneLevel.R \
-                #&& sed -i "s/IMPACT468_targets =/# IMPACT468_targets =/g" geneLevel.R \
-                #&& sed -i "s/setkey(IMPACT410_targets/# setkey(IMPACT410_targets/g" geneLevel.R \
-                #&& sed -i "s/IMPACT341_targets <-/# IMPACT341_targets <-/g" geneLevel.R \
-                #&& sed -i "s/msk_impact_341 <-/# msk_impact_341 <-/g" geneLevel.R \
-                #&& sed -i "s/setnames(IMPACT341_targets/# setnames(IMPACT341_targets/g" geneLevel.R \
-                #&& sed -i "s/setkey(IMPACT341_targets/# setkey(IMPACT341_targets/g" geneLevel.R \
             # copy execs to /usr/bin/facets-suite
                 && mkdir -p /usr/bin/facets-suite/ \
                 && cp -r /tmp/facets-suite-${FACETS_SUITE_VERSION}/* /usr/bin/facets-suite/ \

build/tools.json

@@ -19,7 +19,7 @@
             "0.7.7"
         ],
         "facets": [
-            "1.6.2"
+            "1.6.3"
         ],
         "gatk": [
             "3.3-0"

setup/bin/roslin_analysis_helper.py

@@ -111,7 +111,7 @@ def generate_discrete_copy_number_data(data_directory,output_directory,data_file
             interval_list = targets[assay]['targets_list']
             extra_arg = '--targetFile '+ interval_list
     cna_command_list = []
-    cna_command_list.append('tool.sh --tool facets --version 1.6.2 --language_version default --language python --cmd geneLevel ' + extra_arg + ' -f ' + discrete_copy_number_files_query + ' -m -o ' + output_path)
+    cna_command_list.append('tool.sh --tool facets --version 1.6.3 --language_version default --language python --cmd geneLevel ' + extra_arg + ' -f ' + discrete_copy_number_files_query + ' -m -o ' + output_path)
     cna_command_list.append('mv ' + output_path + ' ' + gene_cna_file)
     cna_command_list.append('mv ' + scna_output_path + ' ' + output_path)
     run_command_list(cna_command_list,'generate_discrete_copy_number')

setup/bin/roslin_resources.json

@@ -163,7 +163,7 @@
             "default": "sing.sh delly 0.7.7"
         },
         "facets": {
-            "1.6.2": "sing.sh facets 1.6.2"
+            "1.6.3": "sing.sh facets 1.6.3"
         },
         "gatk": {
             "3.3-0": "sing.sh gatk 3.3-0",

setup/cwl/modules/pair/facets.cwl

@@ -118,4 +118,4 @@ steps:
       cval: facets_cval
       tumor_id: tumor_sample_name
     out: [png_files, txt_files_purity, txt_files_hisens, out_files, rdata_files, seg_files]
-    run: ../../tools/facets.doFacets/1.6.2/facets.doFacets.cwl
+    run: ../../tools/facets.doFacets/1.6.3/facets.doFacets.cwl

setup/cwl/tools/facets.doFacets/1.6.2/facets.doFacets.cwl → setup/cwl/tools/facets.doFacets/1.6.3/facets.doFacets.cwl

@@ -13,7 +13,7 @@ $schemas:
 doap:release:
 - class: doap:Version
   doap:name: facets.doFacets
-  doap:revision: 1.6.2
+  doap:revision: 1.6.3
 - class: doap:Version
   doap:name: cwl-wrapper
   doap:revision: 1.0.0
@@ -47,7 +47,7 @@ arguments:
 - valueFrom: "facets"
   prefix: --tool
   position: 0
-- valueFrom: "1.6.2"
+- valueFrom: "1.6.3"
   prefix: --version
   position: 0
 - valueFrom: "default"