fix bwa_index

[arvados.git] / crunch_scripts / arvados-bcbio-nextgen.py

diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
old mode 100644 (file)
new mode 100755 (executable)
index cd17a13..fe3c6eb
--- a/crunch_scripts/arvados-bcbio-nextgen.py
+++ b/crunch_scripts/arvados-bcbio-nextgen.py
@@ -15,11 +15,9 @@ t = arvados.current_task().tmpdir
 
 os.unlink("/usr/local/share/bcbio-nextgen/galaxy")
 os.mkdir("/usr/local/share/bcbio-nextgen/galaxy")
-shutil.copy("/usr/local/share/bcbio-nextgen/galaxy/config/bcbio_system.yaml", "/usr/local/share/bcbio-nextgen/galaxy")
+shutil.copy("/usr/local/share/bcbio-nextgen/config/bcbio_system.yaml", "/usr/local/share/bcbio-nextgen/galaxy")
 
-os.mkdir("/usr/local/share/bcbio-nextgen/galaxy/tool-data")
-
-with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/tool_data_table_conf.xml") as f:
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool_data_table_conf.xml", "w") as f:
     f.write('''<tables>
     <!-- Locations of indexes in the BWA mapper format -->
     <table name="bwa_indexes" comment_char="#">
@@ -54,27 +52,54 @@ with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/tool_data_table_conf.
 </tables>
 ''')
 
+os.mkdir("/usr/local/share/bcbio-nextgen/galaxy/tool-data")
+
 with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/bowtie2_indices.loc", "w") as f:
-    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(dir $(bowtie2_indices))"))
+    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(dir $(bowtie2_indices))\n"))
 
-with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/bwa_indices.loc", "w") as f:
-    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(bwa_indices))"))
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/bwa_index.loc", "w") as f:
+    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(bwa_index))\n"))
 
 with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/gatk_sorted_picard_index.loc", "w") as f:
-    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(gatk_sorted_picard_index))"))
+    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(gatk_sorted_picard_index))\n"))
 
 with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/picard_index.loc", "w") as f:
-    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(picard_indices))"))
+    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(picard_index))\n"))
 
 with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/sam_fa_indices.loc", "w") as f:
-    f.write(subst.do_substitution(p, "index\tGRCh37\t$(file $(sam_fa_indices))"))
+    f.write(subst.do_substitution(p, "index\tGRCh37\t$(file $(sam_fa_indices))\n"))
+
+with open("/tmp/crunch-job/gatk-variant.yaml", "w") as f:
+    f.write('''
+# Template for whole genome Illumina variant calling with GATK pipeline
+---
+details:
+  - analysis: variant2
+    genome_build: GRCh37
+    # to do multi-sample variant calling, assign samples the same metadata / batch
+    # metadata:
+    #   batch: your-arbitrary-batch-name
+    algorithm:
+      aligner: bwa
+      mark_duplicates: picard
+      recalibrate: gatk
+      realign: gatk
+      variantcaller: gatk-haplotype
+      platform: illumina
+      quality_format: Standard
+      coverage_interval: genome
+      # for targetted projects, set the region
+      # variant_regions: /path/to/your.bed
+''')
 
 os.chdir(arvados.current_task().tmpdir)
 
-rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "gatk-variant", "project1",
-                         subst.do_substitution(p, "$(R1)"),
-                         subst.do_substitution(p, "$(R2)")])
+rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "/tmp/crunch-job/gatk-variant.yaml", "project1",
+                         subst.do_substitution(p, "$(file $(R1))"),
+                         subst.do_substitution(p, "$(file $(R2))")])
 
 os.chdir("project1/work")
 
-rcode = subprocess.call(["bcbio_nextgen.py", "../config/project1.yaml")])
+os.symlink("/usr/local/share/bcbio-nextgen/galaxy/tool-data", "tool-data")
+
+rcode = subprocess.call(["bcbio_nextgen.py", "../config/project1.yaml"])