First try at bcbio-nextgen script

diff --git a/crunch_scripts/arvados-bcbio-nextgen.py b/crunch_scripts/arvados-bcbio-nextgen.py
new file mode 100644 (file)
index 0000000..cd17a13
--- /dev/null
+++ b/crunch_scripts/arvados-bcbio-nextgen.py
@@ -0,0 +1,80 @@
+#!/usr/bin/python
+
+import arvados
+import subprocess
+import subst
+import shutil
+import os
+
+if len(arvados.current_task()['parameters']) > 0:
+    p = arvados.current_task()['parameters']
+else:
+    p = arvados.current_job()['script_parameters']
+
+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")
+
+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:
+    f.write('''<tables>
+    <!-- Locations of indexes in the BWA mapper format -->
+    <table name="bwa_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bwa_index.loc" />
+    </table>
+    <!-- Locations of indexes in the Bowtie2 mapper format -->
+    <table name="bowtie2_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bowtie2_indices.loc" />
+    </table>
+    <!-- Locations of indexes in the Bowtie2 mapper format for TopHat2 to use -->
+    <table name="tophat2_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bowtie2_indices.loc" />
+    </table>
+    <!-- Location of SAMTools indexes and other files -->
+    <table name="sam_fa_indexes" comment_char="#">
+        <columns>index, value, path</columns>
+        <file path="tool-data/sam_fa_indices.loc" />
+    </table>
+    <!-- Location of Picard dict file and other files -->
+    <table name="picard_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/picard_index.loc" />
+    </table>
+    <!-- Location of Picard dict files valid for GATK -->
+    <table name="gatk_picard_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/gatk_sorted_picard_index.loc" />
+    </table>
+</tables>
+''')
+
+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 $(bowtie2_indices))"))
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/bwa_indices.loc", "w") as f:
+    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(bwa_indices))"))
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/gatk_sorted_picard_index.loc", "w") as f:
+    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(gatk_sorted_picard_index))"))
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/picard_index.loc", "w") as f:
+    f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(picard_indices))"))
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/sam_fa_indices.loc", "w") as f:
+    f.write(subst.do_substitution(p, "index\tGRCh37\t$(file $(sam_fa_indices))"))
+
+os.chdir(arvados.current_task().tmpdir)
+
+rcode = subprocess.call(["bcbio_nextgen.py", "--workflow", "template", "gatk-variant", "project1",
+                         subst.do_substitution(p, "$(R1)"),
+                         subst.do_substitution(p, "$(R2)")])
+
+os.chdir("project1/work")
+
+rcode = subprocess.call(["bcbio_nextgen.py", "../config/project1.yaml")])