updates

- added batch parsing usage - new docker image for environment - bug fixes for error messages & parsing for .fq.gz
genepattern · Jan 4, 2024 · 308201b · 308201b
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commit 308201b
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Showing 28 changed files with 268 additions and 1,135,546 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.gitignore b/.gitignore
@@ -15,3 +15,6 @@ gpunit/.DS_Store
 .DS_Store
 gpunit/.DS_Store
 gpunit/.DS_Store
+src/mosek.lic
+*.bam
+*.bai
diff --git a/AA_bam_files_test/input_list.txt b/AA_bam_files_test/input_list.txt
@@ -0,0 +1,2 @@
+/files/AA_bam_files_test/KT9.cs.bam
+/files/AA_bam_files_test/KT14.cs.bam
diff --git a/Dockerfile b/Dockerfile
@@ -1,6 +1,6 @@
 # Parent image is the Amplicon-Architect-Environment
 # https://hub.docker.com/r/jluebeck/prepareaa/tags
-FROM jluebeck/prepareaa:v1.1.0
+FROM jluebeck/prepareaa:v1.1.3
 
 USER root
 RUN mkdir -p /opt/genepatt
@@ -10,4 +10,14 @@ COPY src/download_ref.sh /opt/genepatt
 ENV MOSEKLM_LICENSE_FILE=/expanse/projects/mesirovlab/genepattern/servers/ucsd.prod/mosek/8/licenses/
 RUN mkdir -p /home/aa_user/mosek
 RUN chmod 777 /opt/genepatt/*
+# RUN chmod 777 /home/aa_user/mosek/
+RUN chmod 777 /home/*
 USER aa_user
+
+# Copy local mosek.lic file, for testing only
+# COPY src/mosek.lic /home/mosek/
+# COPY src/mosek.lic /home/aa_user/mosek/
+
+# ENV MOSEKLM_LICENSE_FILE=/home/mosek
+
+## python3 /files/src/run_aa.py --input /files/AA_bam_files_test/input_list.txt --n_threads 2 --reference hg19 --RUN_AA Yes --RUN_AC Yes --AA_runmode FULL
diff --git a/gpunit/.DS_Store b/gpunit/.DS_Store
diff --git a/gpunit/expected_output/TESTX_H7YRLADXX_S1_L001_AA_CNV_SEEDS.bed b/gpunit/expected_output/TESTX_H7YRLADXX_S1_L001_AA_CNV_SEEDS.bed
diff --git a/gpunit/expected_output/TESTX_H7YRLADXX_S1_L001_AA_results/TESTX_H7YRLADXX_S1_L001.log b/gpunit/expected_output/TESTX_H7YRLADXX_S1_L001_AA_results/TESTX_H7YRLADXX_S1_L001.log
diff --git a/...it/expected_output/TESTX_H7YRLADXX_S1_L001_AA_results/TESTX_H7YRLADXX_S1_L001_summary.txt b/...it/expected_output/TESTX_H7YRLADXX_S1_L001_AA_results/TESTX_H7YRLADXX_S1_L001_summary.txt
diff --git a/gpunit/expected_output/TESTX_H7YRLADXX_S1_L001_aln_stage.stderr b/gpunit/expected_output/TESTX_H7YRLADXX_S1_L001_aln_stage.stderr
diff --git a/...LADXX_S1_L001_classification/TESTX_H7YRLADXX_S1_L001_amplicon_classification_profiles.tsv b/...LADXX_S1_L001_classification/TESTX_H7YRLADXX_S1_L001_amplicon_classification_profiles.tsv
diff --git a/...ed_output/TESTX_H7YRLADXX_S1_L001_classification/TESTX_H7YRLADXX_S1_L001_ecDNA_counts.tsv b/...ed_output/TESTX_H7YRLADXX_S1_L001_classification/TESTX_H7YRLADXX_S1_L001_ecDNA_counts.tsv
diff --git a/...output/TESTX_H7YRLADXX_S1_L001_classification/TESTX_H7YRLADXX_S1_L001_feature_entropy.tsv b/...output/TESTX_H7YRLADXX_S1_L001_classification/TESTX_H7YRLADXX_S1_L001_feature_entropy.tsv
diff --git a/...ected_output/TESTX_H7YRLADXX_S1_L001_classification/TESTX_H7YRLADXX_S1_L001_gene_list.tsv b/...ected_output/TESTX_H7YRLADXX_S1_L001_classification/TESTX_H7YRLADXX_S1_L001_gene_list.tsv
diff --git a/...utput/TESTX_H7YRLADXX_S1_L001_cnvkit_output/GRCh38_cnvkit_filtered_ref.antitarget-tmp.bed b/...utput/TESTX_H7YRLADXX_S1_L001_cnvkit_output/GRCh38_cnvkit_filtered_ref.antitarget-tmp.bed
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		/files/AA_bam_files_test/KT9.cs.bam
		/files/AA_bam_files_test/KT14.cs.bam