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changeset 6:a1d09ab090bb draft

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Uploaded
author sauria
date Thu, 16 Apr 2015 15:57:50 -0400
parents a1ab64129a04
children b17022a25879
files hifive/hifive/complete_fivec_project.xml hifive/hifive/complete_hic_project.xml hifive/hifive/create_fivec_dataset.xml hifive/hifive/create_fivec_fragmentset.xml hifive/hifive/create_fivec_heatmap.xml hifive/hifive/create_fivec_project.xml hifive/hifive/create_hic_dataset.xml hifive/hifive/create_hic_fendset.xml hifive/hifive/create_hic_heatmap.xml hifive/hifive/create_hic_project.xml hifive/hifive/get_interval_fivec_data.xml hifive/hifive/get_interval_hic_data.xml hifive/hifive/learn_fivec_normalization.xml hifive/hifive/learn_hic_normalization.xml hifive/hifive/tool_dependencies.xml
diffstat 15 files changed, 75 insertions(+), 75 deletions(-) [+]
line wrap: on
line diff
--- a/hifive/hifive/complete_fivec_project.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/complete_fivec_project.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="complete_fivec_project" name="analyze_5C_data">
     <requirements>
-        <requirement type='package' name="hifive" version="1.0.2"/>
-        <requirement type='package' name="numpy" version="1.9"/>
-        <requirement type='package' name="scipy" version="0.14"/>
-        <requirement type='package' name="h5py" version="2.4.0"/>
-        <requirement type='package' name="cython" version="0.20.1"/>
+        <requirement type='package' version="1.0.2">hifive</requirement>
+        <requirement type='package' version="1.7">numpy</requirement>
+        <requirement type='package' version="0.12">scipy</requirement>
+        <requirement type='package' version="2.4.0">h5py</requirement>
+        <requirement type='package' version="0.20.1">cython</requirement>
     </requirements>
     <description>from start to finish, including creating a fragmentset, dataset, and corrected HiFive 5C project</description>
     <command>
--- a/hifive/hifive/complete_hic_project.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/complete_hic_project.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="complete_hic_project" name="analyze_HiC_data">
     <requirements>
-        <requirement type='package' name="hifive" version="1.0.2"/>
-        <requirement type='package' name="numpy" version="1.9"/>
-        <requirement type='package' name="scipy" version="0.14"/>
-        <requirement type='package' name="h5py" version="2.4.0"/>
-        <requirement type='package' name="cython" version="0.20.1"/>
+        <requirement type='package' version="1.0.2">hifive</requirement>
+        <requirement type='package' version="1.7">numpy</requirement>
+        <requirement type='package' version="0.12">scipy</requirement>
+        <requirement type='package' version="2.4.0">h5py</requirement>
+        <requirement type='package' version="0.20.1">cython</requirement>
     </requirements>
     <description>from start to finish, including creating a fendset, dataset, and corrected HiFive HiC project</description>
     <command>
--- a/hifive/hifive/create_fivec_dataset.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/create_fivec_dataset.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_fivec_dataset" name="create_5C_dataset">
     <requirements>
-        <requirement type='package' name="hifive" version="1.0.2"/>
-        <requirement type='package' name="numpy" version="1.9"/>
-        <requirement type='package' name="scipy" version="0.14"/>
-        <requirement type='package' name="h5py" version="2.4.0"/>
-        <requirement type='package' name="cython" version="0.20.1"/>
+        <requirement type='package' version="1.0.2">hifive</requirement>
+        <requirement type='package' version="1.7">numpy</requirement>
+        <requirement type='package' version="0.12">scipy</requirement>
+        <requirement type='package' version="2.4.0">h5py</requirement>
+        <requirement type='package' version="0.20.1">cython</requirement>
     </requirements>
     <description>create a HiFive 5C data object</description>
     <command>
--- a/hifive/hifive/create_fivec_fragmentset.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/create_fivec_fragmentset.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_fragmentset" name="create_fragments">
     <requirements>
-        <requirement type='package' name="hifive" version="1.0.2"/>
-        <requirement type='package' name="numpy" version="1.9"/>
-        <requirement type='package' name="scipy" version="0.14"/>
-        <requirement type='package' name="h5py" version="2.4.0"/>
-        <requirement type='package' name="cython" version="0.20.1"/>
+        <requirement type='package' version="1.0.2">hifive</requirement>
+        <requirement type='package' version="1.7">numpy</requirement>
+        <requirement type='package' version="0.12">scipy</requirement>
+        <requirement type='package' version="2.4.0">h5py</requirement>
+        <requirement type='package' version="0.20.1">cython</requirement>
     </requirements>
     <description>create a HiFive fragment object</description>
     <command>hifive fragments -q $input $output</command>
--- a/hifive/hifive/create_fivec_heatmap.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/create_fivec_heatmap.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_fivec_heatmap" name="generate_5C_heatmaps">
     <requirements>
-        <requirement type='package' name="hifive" version="1.0.2"/>
-        <requirement type='package' name="numpy" version="1.9"/>
-        <requirement type='package' name="scipy" version="0.14"/>
-        <requirement type='package' name="h5py" version="2.4.0"/>
-        <requirement type='package' name="cython" version="0.20.1"/>
+        <requirement type='package' version="1.0.2">hifive</requirement>
+        <requirement type='package' version="1.7">numpy</requirement>
+        <requirement type='package' version="0.12">scipy</requirement>
+        <requirement type='package' version="2.4.0">h5py</requirement>
+        <requirement type='package' version="0.20.1">cython</requirement>
     </requirements>
     <description>create an hdf5 dictionary of heatmaps for a HiFive 5C project</description>
     <command>
--- a/hifive/hifive/create_fivec_project.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/create_fivec_project.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_fivec_project" name="create_5C_project">
     <requirements>
-        <requirement type='package' name="hifive" version="1.0.2"/>
-        <requirement type='package' name="numpy" version="1.9"/>
-        <requirement type='package' name="scipy" version="0.14"/>
-        <requirement type='package' name="h5py" version="2.4.0"/>
-        <requirement type='package' name="cython" version="0.20.1"/>
+        <requirement type='package' version="1.0.2">hifive</requirement>
+        <requirement type='package' version="1.7">numpy</requirement>
+        <requirement type='package' version="0.12">scipy</requirement>
+        <requirement type='package' version="2.4.0">h5py</requirement>
+        <requirement type='package' version="0.20.1">cython</requirement>
     </requirements>
     <description>create a HiFive 5C project object</description>
     <command>
--- a/hifive/hifive/create_hic_dataset.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/create_hic_dataset.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_hic_dataset" name="create_HiC_dataset">
     <requirements>
-        <requirement type='package' name="hifive" version="1.0.2"/>
-        <requirement type='package' name="numpy" version="1.9"/>
-        <requirement type='package' name="scipy" version="0.14"/>
-        <requirement type='package' name="h5py" version="2.4.0"/>
-        <requirement type='package' name="cython" version="0.20.1"/>
+        <requirement type='package' version="1.0.2">hifive</requirement>
+        <requirement type='package' version="1.7">numpy</requirement>
+        <requirement type='package' version="0.12">scipy</requirement>
+        <requirement type='package' version="2.4.0">h5py</requirement>
+        <requirement type='package' version="0.20.1">cython</requirement>
     </requirements>
     <description>create a HiFive HiC data object</description>
     <command>
--- a/hifive/hifive/create_hic_fendset.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/create_hic_fendset.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_fendset" name="create_fends">
     <requirements>
-        <requirement type='package' name="hifive" version="1.0.2"/>
-        <requirement type='package' name="numpy" version="1.9"/>
-        <requirement type='package' name="scipy" version="0.14"/>
-        <requirement type='package' name="h5py" version="2.4.0"/>
-        <requirement type='package' name="cython" version="0.20.1"/>
+        <requirement type='package' version="1.0.2">hifive</requirement>
+        <requirement type='package' version="1.7">numpy</requirement>
+        <requirement type='package' version="0.12">scipy</requirement>
+        <requirement type='package' version="2.4.0">h5py</requirement>
+        <requirement type='package' version="0.20.1">cython</requirement>
     </requirements>
     <description>create a HiFive fend object</description>
     <command>hifive fends -q --bed $input $output</command>
--- a/hifive/hifive/create_hic_heatmap.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/create_hic_heatmap.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_hic_heatmap" name="generate_HiC_heatmaps">
     <requirements>
-        <requirement type='package' name="hifive" version="1.0.2"/>
-        <requirement type='package' name="numpy" version="1.9"/>
-        <requirement type='package' name="scipy" version="0.14"/>
-        <requirement type='package' name="h5py" version="2.4.0"/>
-        <requirement type='package' name="cython" version="0.20.1"/>
+        <requirement type='package' version="1.0.2">hifive</requirement>
+        <requirement type='package' version="1.7">numpy</requirement>
+        <requirement type='package' version="0.12">scipy</requirement>
+        <requirement type='package' version="2.4.0">h5py</requirement>
+        <requirement type='package' version="0.20.1">cython</requirement>
     </requirements>
     <description>create an hdf5 dictionary of heatmaps for a HiFive HiC project</description>
     <command>
--- a/hifive/hifive/create_hic_project.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/create_hic_project.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_hic_project" name="create_HiC_project">
     <requirements>
-        <requirement type='package' name="hifive" version="1.0.2"/>
-        <requirement type='package' name="numpy" version="1.9"/>
-        <requirement type='package' name="scipy" version="0.14"/>
-        <requirement type='package' name="h5py" version="2.4.0"/>
-        <requirement type='package' name="cython" version="0.20.1"/>
+        <requirement type='package' version="1.0.2">hifive</requirement>
+        <requirement type='package' version="1.7">numpy</requirement>
+        <requirement type='package' version="0.12">scipy</requirement>
+        <requirement type='package' version="2.4.0">h5py</requirement>
+        <requirement type='package' version="0.20.1">cython</requirement>
     </requirements>
     <description>create a HiFive HiC project object</description>
     <command>
--- a/hifive/hifive/get_interval_fivec_data.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/get_interval_fivec_data.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="get_interval_fivec_data" name="get_interval_5C_data">
     <requirements>
-        <requirement type='package' name="hifive" version="1.0.2"/>
-        <requirement type='package' name="numpy" version="1.9"/>
-        <requirement type='package' name="scipy" version="0.14"/>
-        <requirement type='package' name="h5py" version="2.4.0"/>
-        <requirement type='package' name="cython" version="0.20.1"/>
+        <requirement type='package' version="1.0.2">hifive</requirement>
+        <requirement type='package' version="1.7">numpy</requirement>
+        <requirement type='package' version="0.12">scipy</requirement>
+        <requirement type='package' version="2.4.0">h5py</requirement>
+        <requirement type='package' version="0.20.1">cython</requirement>
     </requirements>
     <description>create an interval file containing 5C data</description>
     <command>
--- a/hifive/hifive/get_interval_hic_data.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/get_interval_hic_data.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="get_interval_hic_data" name="get_interval_HiC_data">
     <requirements>
-        <requirement type='package' name="hifive" version="1.0.2"/>
-        <requirement type='package' name="numpy" version="1.9"/>
-        <requirement type='package' name="scipy" version="0.14"/>
-        <requirement type='package' name="h5py" version="2.4.0"/>
-        <requirement type='package' name="cython" version="0.20.1"/>
+        <requirement type='package' version="1.0.2">hifive</requirement>
+        <requirement type='package' version="1.7">numpy</requirement>
+        <requirement type='package' version="0.12">scipy</requirement>
+        <requirement type='package' version="2.4.0">h5py</requirement>
+        <requirement type='package' version="0.20.1">cython</requirement>
     </requirements>
     <description>create an interval file containing HiC data</description>
     <command>
--- a/hifive/hifive/learn_fivec_normalization.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/learn_fivec_normalization.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="learn_fivec_normalization" name="normalize_5C_project">
     <requirements>
-        <requirement type='package' name="hifive" version="1.0.2"/>
-        <requirement type='package' name="numpy" version="1.9"/>
-        <requirement type='package' name="scipy" version="0.14"/>
-        <requirement type='package' name="h5py" version="2.4.0"/>
-        <requirement type='package' name="cython" version="0.20.1"/>
+        <requirement type='package' version="1.0.2">hifive</requirement>
+        <requirement type='package' version="1.7">numpy</requirement>
+        <requirement type='package' version="0.12">scipy</requirement>
+        <requirement type='package' version="2.4.0">h5py</requirement>
+        <requirement type='package' version="0.20.1">cython</requirement>
     </requirements>
     <description>learn fragment normalization values using probablistic approach</description>
     <command>
--- a/hifive/hifive/learn_hic_normalization.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/learn_hic_normalization.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="learn_hic_normalization" name="normalize_HiC_project">
     <requirements>
-        <requirement type='package' name="hifive" version="1.0.2"/>
-        <requirement type='package' name="numpy" version="1.9"/>
-        <requirement type='package' name="scipy" version="0.14"/>
-        <requirement type='package' name="h5py" version="2.4.0"/>
-        <requirement type='package' name="cython" version="0.20.1"/>
+        <requirement type='package' version="1.0.2">hifive</requirement>
+        <requirement type='package' version="1.7">numpy</requirement>
+        <requirement type='package' version="0.12">scipy</requirement>
+        <requirement type='package' version="2.4.0">h5py</requirement>
+        <requirement type='package' version="0.20.1">cython</requirement>
     </requirements>
     <description>learn fend normalization values using probablistic approach</description>
     <command>
--- a/hifive/hifive/tool_dependencies.xml	Thu Apr 16 15:17:35 2015 -0400
+++ b/hifive/hifive/tool_dependencies.xml	Thu Apr 16 15:57:50 2015 -0400
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="scipy" version="0.14">
-        <repository changeset_revision="2e3809844979" name="package_scipy_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="scipy" version="0.12">
+        <repository changeset_revision="d607515b0510" name="package_scipy_0_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="numpy" version="1.9">
-        <repository name="package_numpy_1_9" owner="iuc" changeset_revision="266529386609" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="True" />
+    <package name="numpy" version="1.7">
+        <repository name="package_numpy_1_7" owner="iuc" changeset_revision="11099cc214d5" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="True" />
     </package>
     <package name="cython" version="0.20.1">
         <repository name="package_cython_0_20_1" owner="iuc" changeset_revision="749f11b9358a" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="True"/>
@@ -13,7 +13,7 @@
         <repository changeset_revision="79b31a4c757c" name="package_h5py_2_4_0" owner="sauria" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="hifive" version="1.0.2">
-        <repository changeset_revision="3dfc9498f211" name="package_hifive_1_0_2" owner="sauria" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="18a457921969" name="package_hifive_1_0_2" owner="sauria" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <set_environment version="1.0">
         <environment_variable action="set_to" name="HIFIVE_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>