Mercurial > repos > bgruening > chemical_data_sources

changeset 2:b65518a007fa draft

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Uploaded
author bgruening
date Sun, 08 Sep 2013 09:42:57 -0400
parents 17a3f755d472
children 021f0ef9474f
files get_pubchem/get_pubchem_as_smiles.py get_pubchem/get_pubchem_as_smiles.xml tool_dependencies.xml
diffstat 3 files changed, 11 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/get_pubchem/get_pubchem_as_smiles.py	Wed Aug 21 03:07:12 2013 -0400
+++ b/get_pubchem/get_pubchem_as_smiles.py	Sun Sep 08 09:42:57 2013 -0400
@@ -13,7 +13,7 @@
 import tempfile
 import shutil
 
-def main(output, processors = 10):
+def main(output, processors = 4):
     output_handle = open(output,'w+')
 
     td = tempfile.mkdtemp()
--- a/get_pubchem/get_pubchem_as_smiles.xml	Wed Aug 21 03:07:12 2013 -0400
+++ b/get_pubchem/get_pubchem_as_smiles.xml	Sun Sep 08 09:42:57 2013 -0400
@@ -1,9 +1,12 @@
 <tool id="ctb_pubchem_download_as_smiles" name="PubChem Download" Version="0.1" >
   <description>as canonical SMILES</description>
+  <requirements>
+    <requirement type="package" version="2.3.2">openbabel</requirement>
+  </requirements>
   <command interpreter="python">
         get_pubchem_as_smiles.py 
             -o $pubchem_smi 
-            -p 10
+            -p 4
             2>&#38;1
   </command>
   <inputs>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sun Sep 08 09:42:57 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="openbabel" version="2.3.2">
+        <repository changeset_revision="99a10425de93" name="package_openbabel_2_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>