Mercurial > repos > sauria > hifive

changeset 5:a1ab64129a04 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author sauria
date Thu, 16 Apr 2015 15:17:35 -0400
parents 05320ceddead
children a1d09ab090bb
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
diffstat 14 files changed, 70 insertions(+), 70 deletions(-) [+]
line wrap: on
line diff
--- a/hifive/hifive/complete_fivec_project.xml	Thu Apr 16 15:13:44 2015 -0400
+++ b/hifive/hifive/complete_fivec_project.xml	Thu Apr 16 15:17:35 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="complete_fivec_project" name="analyze_5C_data">
     <requirements>
-        <requirement type='package' name="hifive"/>
-        <requirement type='package' name="numpy"/>
-        <requirement type='package' name="scipy"/>
-        <requirement type='package' name="h5py"/>
-        <requirement type='package' name="cython"/>
+        <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"/>
     </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 15:13:44 2015 -0400
+++ b/hifive/hifive/complete_hic_project.xml	Thu Apr 16 15:17:35 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="complete_hic_project" name="analyze_HiC_data">
     <requirements>
-        <requirement type='package' name="hifive"/>
-        <requirement type='package' name="numpy"/>
-        <requirement type='package' name="scipy"/>
-        <requirement type='package' name="h5py"/>
-        <requirement type='package' name="cython"/>
+        <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"/>
     </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 15:13:44 2015 -0400
+++ b/hifive/hifive/create_fivec_dataset.xml	Thu Apr 16 15:17:35 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_fivec_dataset" name="create_5C_dataset">
     <requirements>
-        <requirement type='package' name="hifive"/>
-        <requirement type='package' name="numpy"/>
-        <requirement type='package' name="scipy"/>
-        <requirement type='package' name="h5py"/>
-        <requirement type='package' name="cython"/>
+        <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"/>
     </requirements>
     <description>create a HiFive 5C data object</description>
     <command>
--- a/hifive/hifive/create_fivec_fragmentset.xml	Thu Apr 16 15:13:44 2015 -0400
+++ b/hifive/hifive/create_fivec_fragmentset.xml	Thu Apr 16 15:17:35 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_fragmentset" name="create_fragments">
     <requirements>
-        <requirement type='package' name="hifive"/>
-        <requirement type='package' name="numpy"/>
-        <requirement type='package' name="scipy"/>
-        <requirement type='package' name="h5py"/>
-        <requirement type='package' name="cython"/>
+        <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"/>
     </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 15:13:44 2015 -0400
+++ b/hifive/hifive/create_fivec_heatmap.xml	Thu Apr 16 15:17:35 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_fivec_heatmap" name="generate_5C_heatmaps">
     <requirements>
-        <requirement type='package' name="hifive"/>
-        <requirement type='package' name="numpy"/>
-        <requirement type='package' name="scipy"/>
-        <requirement type='package' name="h5py"/>
-        <requirement type='package' name="cython"/>
+        <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"/>
     </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 15:13:44 2015 -0400
+++ b/hifive/hifive/create_fivec_project.xml	Thu Apr 16 15:17:35 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_fivec_project" name="create_5C_project">
     <requirements>
-        <requirement type='package' name="hifive"/>
-        <requirement type='package' name="numpy"/>
-        <requirement type='package' name="scipy"/>
-        <requirement type='package' name="h5py"/>
-        <requirement type='package' name="cython"/>
+        <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"/>
     </requirements>
     <description>create a HiFive 5C project object</description>
     <command>
--- a/hifive/hifive/create_hic_dataset.xml	Thu Apr 16 15:13:44 2015 -0400
+++ b/hifive/hifive/create_hic_dataset.xml	Thu Apr 16 15:17:35 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_hic_dataset" name="create_HiC_dataset">
     <requirements>
-        <requirement type='package' name="hifive"/>
-        <requirement type='package' name="numpy"/>
-        <requirement type='package' name="scipy"/>
-        <requirement type='package' name="h5py"/>
-        <requirement type='package' name="cython"/>
+        <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"/>
     </requirements>
     <description>create a HiFive HiC data object</description>
     <command>
--- a/hifive/hifive/create_hic_fendset.xml	Thu Apr 16 15:13:44 2015 -0400
+++ b/hifive/hifive/create_hic_fendset.xml	Thu Apr 16 15:17:35 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_fendset" name="create_fends">
     <requirements>
-        <requirement type='package' name="hifive"/>
-        <requirement type='package' name="numpy"/>
-        <requirement type='package' name="scipy"/>
-        <requirement type='package' name="h5py"/>
-        <requirement type='package' name="cython"/>
+        <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"/>
     </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 15:13:44 2015 -0400
+++ b/hifive/hifive/create_hic_heatmap.xml	Thu Apr 16 15:17:35 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_hic_heatmap" name="generate_HiC_heatmaps">
     <requirements>
-        <requirement type='package' name="hifive"/>
-        <requirement type='package' name="numpy"/>
-        <requirement type='package' name="scipy"/>
-        <requirement type='package' name="h5py"/>
-        <requirement type='package' name="cython"/>
+        <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"/>
     </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 15:13:44 2015 -0400
+++ b/hifive/hifive/create_hic_project.xml	Thu Apr 16 15:17:35 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="create_hic_project" name="create_HiC_project">
     <requirements>
-        <requirement type='package' name="hifive"/>
-        <requirement type='package' name="numpy"/>
-        <requirement type='package' name="scipy"/>
-        <requirement type='package' name="h5py"/>
-        <requirement type='package' name="cython"/>
+        <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"/>
     </requirements>
     <description>create a HiFive HiC project object</description>
     <command>
--- a/hifive/hifive/get_interval_fivec_data.xml	Thu Apr 16 15:13:44 2015 -0400
+++ b/hifive/hifive/get_interval_fivec_data.xml	Thu Apr 16 15:17:35 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="get_interval_fivec_data" name="get_interval_5C_data">
     <requirements>
-        <requirement type='package' name="hifive"/>
-        <requirement type='package' name="numpy"/>
-        <requirement type='package' name="scipy"/>
-        <requirement type='package' name="h5py"/>
-        <requirement type='package' name="cython"/>
+        <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"/>
     </requirements>
     <description>create an interval file containing 5C data</description>
     <command>
--- a/hifive/hifive/get_interval_hic_data.xml	Thu Apr 16 15:13:44 2015 -0400
+++ b/hifive/hifive/get_interval_hic_data.xml	Thu Apr 16 15:17:35 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="get_interval_hic_data" name="get_interval_HiC_data">
     <requirements>
-        <requirement type='package' name="hifive"/>
-        <requirement type='package' name="numpy"/>
-        <requirement type='package' name="scipy"/>
-        <requirement type='package' name="h5py"/>
-        <requirement type='package' name="cython"/>
+        <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"/>
     </requirements>
     <description>create an interval file containing HiC data</description>
     <command>
--- a/hifive/hifive/learn_fivec_normalization.xml	Thu Apr 16 15:13:44 2015 -0400
+++ b/hifive/hifive/learn_fivec_normalization.xml	Thu Apr 16 15:17:35 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="learn_fivec_normalization" name="normalize_5C_project">
     <requirements>
-        <requirement type='package' name="hifive"/>
-        <requirement type='package' name="numpy"/>
-        <requirement type='package' name="scipy"/>
-        <requirement type='package' name="h5py"/>
-        <requirement type='package' name="cython"/>
+        <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"/>
     </requirements>
     <description>learn fragment normalization values using probablistic approach</description>
     <command>
--- a/hifive/hifive/learn_hic_normalization.xml	Thu Apr 16 15:13:44 2015 -0400
+++ b/hifive/hifive/learn_hic_normalization.xml	Thu Apr 16 15:17:35 2015 -0400
@@ -1,10 +1,10 @@
 <tool id="learn_hic_normalization" name="normalize_HiC_project">
     <requirements>
-        <requirement type='package' name="hifive"/>
-        <requirement type='package' name="numpy"/>
-        <requirement type='package' name="scipy"/>
-        <requirement type='package' name="h5py"/>
-        <requirement type='package' name="cython"/>
+        <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"/>
     </requirements>
     <description>learn fend normalization values using probablistic approach</description>
     <command>