# HG changeset patch
# User charles-bernard
# Date 1477574261 14400
# Node ID 54c2c66e45a9fe20c0df7699730a1d34741dd443
# Parent  6cfa38b014c10b82f4b459e7a10fae11200e2c12
Uploaded

diff -r 6cfa38b014c1 -r 54c2c66e45a9 data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py
--- a/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py	Thu Oct 27 06:55:32 2016 -0400
+++ b/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py	Thu Oct 27 09:17:41 2016 -0400
@@ -231,6 +231,7 @@
     logging.info("*** Intial dictionary")
     logging.info("%s" % params)
 
+
     shutil.copyfile(stranded_index_name, os.path.join(target_directory, stranded_index_name))
     shutil.copyfile(unstranded_index_name, os.path.join(target_directory, unstranded_index_name))
     shutil.copyfile(log_file_name, os.path.join(target_directory, log_file_name))
diff -r 6cfa38b014c1 -r 54c2c66e45a9 data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml
--- a/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml	Thu Oct 27 06:55:32 2016 -0400
+++ b/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml	Thu Oct 27 09:17:41 2016 -0400
@@ -1,6 +1,12 @@
 <tool id="build_alfa_indexes" name="ALFA indexes" version="0.0.1" tool_type="manage_data">
   <description>build ALFA indexes from automatically downloaded gtf annotation file</description>
-
+    <!-- ALFA requires bedtools suite v2.20.0 and above -->
+  <requirements>
+      <requirement type="package" version="2.24">bedtools</requirement>
+      <requirement type="package" version="1.2">samtools</requirement>
+      <requirement type="package" version="1.4">matplotlib</requirement>
+  </requirements>
+  
   <command interpreter="python">data_manager_build_alfa_indexes.py -e "${reference_source['kingdom']}" "${reference_source['species_name']}" -o "${out_file}" $__root_dir__ $__tool_directory__</command>
 
   <inputs>
diff -r 6cfa38b014c1 -r 54c2c66e45a9 data_manager_build_alfa_indexes/tool-data/alfa_indexes.loc.sample~
--- a/data_manager_build_alfa_indexes/tool-data/alfa_indexes.loc.sample~	Thu Oct 27 06:55:32 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-#<species>	<version>	<release>	<value>	<dbkey>	<name>	<prefix>
-#Arabidopsis_thaliana	TAIR10	30	Arabidopsis_t_TAIR10_30	Arabidopsis_t_TAIR10_30	Arabidopsis thaliana: TAIR10	<path_to_alfa_indexes>/Arabidopsis_thaliana.TAIR10.30
-#Drosophila_melanogaster	dm6	30	Drosophila_m_dm6_30	Drosophila_m_dm6_30	Drosophila melanogaster: dm6	<path_to_alfa_indexes>/Drosophila_melanogaster.BDGP6.30
-#Homo_sapiens	v38	82	Homo_s_v38_82	Homo_s_v38_82	Homo sapiens: v38	<path_to_alfa_indexes>/Homo_sapiens.GRCh38.82
-#Mus_musculus	v38	83	Mus_m_v38_83	Mus_m_v38_83	Mus musculus: v38 	<path_to_alfa_indexes>/Mus_musculus.GRCm38.83.chr
diff -r 6cfa38b014c1 -r 54c2c66e45a9 data_manager_build_alfa_indexes/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_build_alfa_indexes/tool_dependencies.xml	Thu Oct 27 09:17:41 2016 -0400
@@ -0,0 +1,11 @@
+<tool_dependency>
+	<package name="bedtools" version="2.24">
+		<repository changeset_revision="3416a1d4a582" name="package_bedtools_2_24" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+	</package>
+    <package name="samtools" version="1.2">
+    	<repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="matplotlib" version="1.4">
+    	<repository changeset_revision="f7424e1cf115" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
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