changeset 8:147814e45209

Uploaded

--- a/align-it/align-it.xml	Thu May 23 17:30:47 2013 -0400
+++ b/align-it/align-it.xml	Sat May 25 12:56:15 2013 -0400
@@ -2,6 +2,7 @@
     <description>and Optimization (Align-it)</description>
     <requirements>
         <requirement type="package" version="1.0.0">silicos_it</requirement>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command>
         align-it --format ${database.ext} --dbase $database --pharmacophore $alignedPharmacophores --dbType 'MOL' --scores $result --epsilon $0epsilon $merge $noHybrid $withExclusion 2>&#38;1

--- a/align-it/alignit_create_db.xml	Thu May 23 17:30:47 2013 -0400
+++ b/align-it/alignit_create_db.xml	Sat May 25 12:56:15 2013 -0400
@@ -2,6 +2,7 @@
     <description>database building (Align-it)</description>
     <requirements>
         <requirement type="package" version="1.0.0">silicos_it</requirement>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command >
         align-it --format ${database.ext} -d $database -p $Pharmacophores --dbType MOL 2>&#38;1

--- a/qed/silicos_qed.xml	Thu May 23 17:30:47 2013 -0400
+++ b/qed/silicos_qed.xml	Sat May 25 12:56:15 2013 -0400
@@ -3,6 +3,8 @@
   <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
   <requirements>
     <requirement type="package" version="1.0.0">silicos_it</requirement>
+    <requirement type="package" version="2012_12_1">rdkit</requirement>
+    <requirement type="package" version="1.7.1">numpy</requirement>
   </requirements>
   <command interpreter="python">qed.py -i "${infile}" --method "${method}" -o "${outfile}" $header 2>&#38;1</command>
   <inputs>

--- a/repository_dependencies.xml	Thu May 23 17:30:47 2013 -0400
+++ b/repository_dependencies.xml	Sat May 25 12:56:15 2013 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
-    <repository changeset_revision="bd886859b184" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="c5383bd4d006" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 </repositories>

--- a/shape-it/shape-it.xml	Thu May 23 17:30:47 2013 -0400
+++ b/shape-it/shape-it.xml	Sat May 25 12:56:15 2013 -0400
@@ -2,6 +2,7 @@
     <description> alignment of a reference molecule against a database of molecules using the shape of the molecules</description>
     <requirements>
         <requirement type="package" version="1.0.0">silicos_it</requirement>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command >
         shape-it --Format ${database.ext}  --dbase $database --reference $reference --addIterations $addIterations --best $best --out $output  2>&#38;1

--- a/strip-it/strip-it.xml	Thu May 23 17:30:47 2013 -0400
+++ b/strip-it/strip-it.xml	Sat May 25 12:56:15 2013 -0400
@@ -1,10 +1,11 @@
 <tool id="stripit" name="Strip-it" version="1.0.0">
     <description> extracts predefined scaffolds from molecules</description>
     <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
         <requirement type="package" version="1.0.0">silicos_it</requirement>
     </requirements>
     <command>
-        strip-it --inputFormat ${infile.ext} --input $infile --output $outfile --noLog
+        strip-it --inputFormat ${infile.ext} --input $infile --output $outfile --noLog 2>&#38;1
     </command>
     <inputs>
         <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" />

--- a/tool_dependencies.xml	Thu May 23 17:30:47 2013 -0400
+++ b/tool_dependencies.xml	Sat May 25 12:56:15 2013 -0400
@@ -7,7 +7,7 @@
         <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="rdkit" version="2012_12_1">
-        <repository changeset_revision="5685fab7ecc2" name="package_rdkit_2012_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="87b2d2831a31" name="package_rdkit_2012_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="silicos_it" version="1.0.0">
         <install version="1.0">