fix: lots of fixes. Mainly py2 -> py3

stjude_warden_bam/resources/app_data/internal_source/warden_combine_counts/resources/usr/bin/process_count_files.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import os
 import sys
@@ -117,7 +117,7 @@
     got_feature_list = True
 print("done getting features")
 samples_ordered = []
-for key, value in sorted(samples.items(), key=lambda k, v: (v, k)):
+for key, value in sorted(samples.items(), key=lambda kv: kv[1]):
     samples_ordered.append(key)
 header_line = count_header_list[0]
 for s in samples_ordered:

stjude_warden_bam/resources/app_data/internal_source/warden_genome_coverage_bed/resources/usr/bin/get_mapped_counts.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import sys
 import re
 

stjude_warden_bam/resources/app_data/internal_source/warden_genome_coverage_bed/src/warden_genome_coverage_bed.sh

@@ -42,7 +42,7 @@ main() {
 
     default_scale=0
     if [ "$scale" == "$default_scale" ]; then
-        scale=$(python -c "print float(10**7)/float($counts)")
+        scale=$(python3 -c "print(float(10**7)/float($counts))")
     else
         scale=1
     fi

stjude_warden_bam/resources/app_data/internal_source/warden_htseq_count/resources/usr/bin/calc_fpkm.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import sys
 from decimal import *

stjude_warden_bam/resources/app_data/internal_source/warden_htseq_count/src/warden_htseq_count.sh

@@ -3,13 +3,7 @@
 set -e -x -o pipefail
 
 main() {
-    python -m pip install --no-cache-dir --upgrade pip~=20.3.4
-    python -m pip install --no-cache-dir --no-python-version-warning --upgrade setuptools~=44.1
-    python -m pip install --no-cache-dir --no-python-version-warning functools32~=3.2
-    python -m pip install --no-cache-dir --no-python-version-warning numpy==1.16.6
-    python -m pip install --no-cache-dir --no-python-version-warning matplotlib==2.2.5
-    python -m pip install --no-cache-dir --no-python-version-warning pysam==0.16.0.1
-    python -m pip install --no-cache-dir --no-python-version-warning HTSeq==0.12.4
+    python3 -m pip install --no-cache-dir HTSeq
     wget -nv -O jq-1.6 https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64
     chmod +x ./jq-1.6
 
@@ -33,7 +27,7 @@ main() {
     if [ -n "$gene_length_file" ] && [ "$id_attribute" = "gene_name" ]; then
         fpkm_file=$prefix.fpkm.txt
         fpkmlog2File=$prefix.fpkm.log2.txt
-        python /usr/bin/calc_fpkm.py "$out_name" "$gene_length_file_path" "$fpkm_file" "$fpkmlog2File"
+        python3 /usr/bin/calc_fpkm.py "$out_name" "$gene_length_file_path" "$fpkm_file" "$fpkmlog2File"
 
         dx mkdir -p FPKM
         fpkm=$(dx upload --path FPKM/ "$fpkm_file" --brief)

stjude_warden_bam/resources/app_data/internal_source/warden_simple_differential_expression/resources/usr/bin/parse_contrasts.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import sys
 
 

stjude_warden_bam/resources/app_data/internal_source/warden_voom_limma/resources/usr/bin/parse_contrasts.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import sys
 
 

stjude_warden_bam/resources/app_data/internal_source/warden_voom_limma/resources/usr/bin/parse_voom_limma_params.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import yaml
 import sys

stjude_warden_bam/resources/usr/bin/create_workflow.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # warden_python 1.1.0
 
 

stjude_warden_bam/resources/usr/bin/parse_excel_sample_list.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import openpyxl
 import csv

stjude_warden_bam/resources/usr/bin/process_files.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import sys
 import os

stjude_warden_bam/src/warden.sh

@@ -74,7 +74,7 @@ main() {
     if [ "$sample_list_extension" == "txt" ]; then
         dos2unix -q sample_list.txt
     elif [ "$sample_list_extension" == "xlsx" ]; then
-        python /usr/bin/parse_excel_sample_list.py sample_list.xlsx > sample_list.txt
+        python3 /usr/bin/parse_excel_sample_list.py sample_list.xlsx > sample_list.txt
     else
         dx-jobutil-report-error "Improper Sample List Extension. This should be a .txt or .xlsx file" AppError
     fi

stjude_warden_counts/resources/app_data/internal_source/warden_combine_counts/resources/usr/bin/process_count_files.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import os
 import sys
@@ -117,7 +117,7 @@
     got_feature_list = True
 print("done getting features")
 samples_ordered = []
-for key, value in sorted(samples.items(), key=lambda k, v: (v, k)):
+for key, value in sorted(samples.items(), key=lambda kv: kv[1]):
     samples_ordered.append(key)
 header_line = count_header_list[0]
 for s in samples_ordered:

stjude_warden_counts/resources/app_data/internal_source/warden_simple_differential_expression/resources/usr/bin/parse_contrasts.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import sys
 
 

stjude_warden_counts/resources/app_data/internal_source/warden_voom_limma/resources/usr/bin/parse_contrasts.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import sys
 
 

stjude_warden_counts/resources/app_data/internal_source/warden_voom_limma/resources/usr/bin/parse_voom_limma_params.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import yaml
 import sys

stjude_warden_counts/resources/usr/bin/create_workflow.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # warden_python 1.1.0
 
 

stjude_warden_counts/resources/usr/bin/parse_excel_sample_list.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import openpyxl
 import csv

stjude_warden_counts/resources/usr/bin/process_files.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import sys
 import os

stjude_warden_counts/src/warden.sh

@@ -45,7 +45,7 @@ main() {
     if [ "$sample_list_extension" == "txt" ]; then
         dos2unix -q sample_list.txt
     elif [ "$sample_list_extension" == "xlsx" ]; then
-        python /usr/bin/parse_excel_sample_list.py sample_list.xlsx > sample_list.txt
+        python3 /usr/bin/parse_excel_sample_list.py sample_list.xlsx > sample_list.txt
     else
         dx-jobutil-report-error "Improper Sample List Extension. This should be a .txt or .xlsx file" AppError
     fi

stjude_warden_fastq/resources/app_data/internal_source/warden_combine_counts/resources/usr/bin/process_count_files.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import os
 import sys
@@ -117,7 +117,7 @@
     got_feature_list = True
 print("done getting features")
 samples_ordered = []
-for key, value in sorted(samples.items(), key=lambda k, v: (v, k)):
+for key, value in sorted(samples.items(), key=lambda kv: kv[1]):
     samples_ordered.append(key)
 header_line = count_header_list[0]
 for s in samples_ordered:

stjude_warden_fastq/resources/app_data/internal_source/warden_combine_flagstat/resources/usr/bin/process_flagstat.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import sys
 import os

stjude_warden_fastq/resources/app_data/internal_source/warden_genome_coverage_bed/resources/usr/bin/get_mapped_counts.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import sys
 import re
 

stjude_warden_fastq/resources/app_data/internal_source/warden_genome_coverage_bed/src/warden_genome_coverage_bed.sh

@@ -35,7 +35,7 @@ main() {
 
     default_scale=0
     if [ "$scale" == "$default_scale" ]; then
-        scale=$(python -c "print float(10**7)/float($counts)")
+        scale=$(python3 -c "print(float(10**7)/float($counts))")
     else
         scale=1
     fi

stjude_warden_fastq/resources/app_data/internal_source/warden_htseq_count/resources/usr/bin/calc_fpkm.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import sys
 from decimal import *

stjude_warden_fastq/resources/app_data/internal_source/warden_htseq_count/src/warden_htseq_count.sh

@@ -3,13 +3,7 @@
 set -e -x -o pipefail
 
 main() {
-    python -m pip install --no-cache-dir --upgrade pip~=20.3.4
-    python -m pip install --no-cache-dir --no-python-version-warning --upgrade setuptools~=44.1
-    python -m pip install --no-cache-dir --no-python-version-warning functools32~=3.2
-    python -m pip install --no-cache-dir --no-python-version-warning numpy==1.16.6
-    python -m pip install --no-cache-dir --no-python-version-warning matplotlib==2.2.5
-    python -m pip install --no-cache-dir --no-python-version-warning pysam==0.16.0.1
-    python -m pip install --no-cache-dir --no-python-version-warning HTSeq==0.12.4
+    python3 -m pip install --no-cache-dir HTSeq
     wget -nv -O jq-1.6 https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64
     chmod +x ./jq-1.6
 
@@ -33,7 +27,7 @@ main() {
     if [ -n "$gene_length_file" ] && [ "$id_attribute" = "gene_name" ]; then
         fpkm_file=$prefix.fpkm.txt
         fpkmlog2File=$prefix.fpkm.log2.txt
-        python /usr/bin/calc_fpkm.py "$out_name" "$gene_length_file_path" "$fpkm_file" "$fpkmlog2File"
+        python3 /usr/bin/calc_fpkm.py "$out_name" "$gene_length_file_path" "$fpkm_file" "$fpkmlog2File"
 
         dx mkdir -p FPKM
         fpkm=$(dx upload --path FPKM/ "$fpkm_file" --brief)

stjude_warden_fastq/resources/app_data/internal_source/warden_simple_differential_expression/resources/usr/bin/parse_contrasts.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import sys
 
 

stjude_warden_fastq/resources/app_data/internal_source/warden_voom_limma/resources/usr/bin/parse_contrasts.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import sys
 
 

stjude_warden_fastq/resources/app_data/internal_source/warden_voom_limma/resources/usr/bin/parse_voom_limma_params.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import yaml
 import sys

stjude_warden_fastq/resources/usr/bin/create_workflow.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # warden_python 1.1.0
 
 

stjude_warden_fastq/resources/usr/bin/parse_excel_sample_list.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import openpyxl
 import csv

stjude_warden_fastq/resources/usr/bin/process_files.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import sys
 import os

stjude_warden_fastq/src/warden.sh

@@ -74,7 +74,7 @@ main() {
     if [ "$sample_list_extension" == "txt" ]; then
         dos2unix -q sample_list.txt
     elif [ "$sample_list_extension" == "xlsx" ]; then
-        python /usr/bin/parse_excel_sample_list.py sample_list.xlsx > sample_list.txt
+        python3 /usr/bin/parse_excel_sample_list.py sample_list.xlsx > sample_list.txt
     else
         dx-jobutil-report-error "Improper Sample List Extension. This should be a .txt or .xlsx file" AppError
     fi