Mercurial > repos > sauria > hifive
changeset 7:b17022a25879 draft
Uploaded
author | sauria |
---|---|
date | Thu, 16 Apr 2015 16:35:12 -0400 |
parents | a1d09ab090bb |
children | 5d96a89cd820 |
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, 47 insertions(+), 50 deletions(-) [+] |
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--- a/hifive/hifive/complete_fivec_project.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/complete_fivec_project.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,9 +1,9 @@ <tool id="complete_fivec_project" name="analyze_5C_data"> <requirements> <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="1.7.1">numpy</requirement> + <requirement type='package' version="0.12.0">scipy</requirement> + <requirement type='package' version="2.5.0">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>
--- a/hifive/hifive/complete_hic_project.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/complete_hic_project.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,9 +1,9 @@ <tool id="complete_hic_project" name="analyze_HiC_data"> <requirements> <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="1.7.1">numpy</requirement> + <requirement type='package' version="0.12.0">scipy</requirement> + <requirement type='package' version="2.5.0">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>
--- a/hifive/hifive/create_fivec_dataset.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/create_fivec_dataset.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,9 +1,9 @@ <tool id="create_fivec_dataset" name="create_5C_dataset"> <requirements> <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="1.7.1">numpy</requirement> + <requirement type='package' version="0.12.0">scipy</requirement> + <requirement type='package' version="2.5.0">h5py</requirement> <requirement type='package' version="0.20.1">cython</requirement> </requirements> <description>create a HiFive 5C data object</description>
--- a/hifive/hifive/create_fivec_fragmentset.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/create_fivec_fragmentset.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,9 +1,9 @@ <tool id="create_fragmentset" name="create_fragments"> <requirements> <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="1.7.1">numpy</requirement> + <requirement type='package' version="0.12.0">scipy</requirement> + <requirement type='package' version="2.5.0">h5py</requirement> <requirement type='package' version="0.20.1">cython</requirement> </requirements> <description>create a HiFive fragment object</description>
--- a/hifive/hifive/create_fivec_heatmap.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/create_fivec_heatmap.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,9 +1,9 @@ <tool id="create_fivec_heatmap" name="generate_5C_heatmaps"> <requirements> <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="1.7.1">numpy</requirement> + <requirement type='package' version="0.12.0">scipy</requirement> + <requirement type='package' version="2.5.0">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>
--- a/hifive/hifive/create_fivec_project.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/create_fivec_project.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,9 +1,9 @@ <tool id="create_fivec_project" name="create_5C_project"> <requirements> <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="1.7.1">numpy</requirement> + <requirement type='package' version="0.12.0">scipy</requirement> + <requirement type='package' version="2.5.0">h5py</requirement> <requirement type='package' version="0.20.1">cython</requirement> </requirements> <description>create a HiFive 5C project object</description>
--- a/hifive/hifive/create_hic_dataset.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/create_hic_dataset.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,9 +1,9 @@ <tool id="create_hic_dataset" name="create_HiC_dataset"> <requirements> <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="1.7.1">numpy</requirement> + <requirement type='package' version="0.12.0">scipy</requirement> + <requirement type='package' version="2.5.0">h5py</requirement> <requirement type='package' version="0.20.1">cython</requirement> </requirements> <description>create a HiFive HiC data object</description>
--- a/hifive/hifive/create_hic_fendset.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/create_hic_fendset.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,9 +1,9 @@ <tool id="create_fendset" name="create_fends"> <requirements> <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="1.7.1">numpy</requirement> + <requirement type='package' version="0.12.0">scipy</requirement> + <requirement type='package' version="2.5.0">h5py</requirement> <requirement type='package' version="0.20.1">cython</requirement> </requirements> <description>create a HiFive fend object</description>
--- a/hifive/hifive/create_hic_heatmap.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/create_hic_heatmap.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,9 +1,9 @@ <tool id="create_hic_heatmap" name="generate_HiC_heatmaps"> <requirements> <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="1.7.1">numpy</requirement> + <requirement type='package' version="0.12.0">scipy</requirement> + <requirement type='package' version="2.5.0">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>
--- a/hifive/hifive/create_hic_project.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/create_hic_project.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,9 +1,9 @@ <tool id="create_hic_project" name="create_HiC_project"> <requirements> <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="1.7.1">numpy</requirement> + <requirement type='package' version="0.12.0">scipy</requirement> + <requirement type='package' version="2.5.0">h5py</requirement> <requirement type='package' version="0.20.1">cython</requirement> </requirements> <description>create a HiFive HiC project object</description>
--- a/hifive/hifive/get_interval_fivec_data.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/get_interval_fivec_data.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,9 +1,9 @@ <tool id="get_interval_fivec_data" name="get_interval_5C_data"> <requirements> <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="1.7.1">numpy</requirement> + <requirement type='package' version="0.12.0">scipy</requirement> + <requirement type='package' version="2.5.0">h5py</requirement> <requirement type='package' version="0.20.1">cython</requirement> </requirements> <description>create an interval file containing 5C data</description>
--- a/hifive/hifive/get_interval_hic_data.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/get_interval_hic_data.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,9 +1,9 @@ <tool id="get_interval_hic_data" name="get_interval_HiC_data"> <requirements> <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="1.7.1">numpy</requirement> + <requirement type='package' version="0.12.0">scipy</requirement> + <requirement type='package' version="2.5.0">h5py</requirement> <requirement type='package' version="0.20.1">cython</requirement> </requirements> <description>create an interval file containing HiC data</description>
--- a/hifive/hifive/learn_fivec_normalization.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/learn_fivec_normalization.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,9 +1,9 @@ <tool id="learn_fivec_normalization" name="normalize_5C_project"> <requirements> <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="1.7.1">numpy</requirement> + <requirement type='package' version="0.12.0">scipy</requirement> + <requirement type='package' version="2.5.0">h5py</requirement> <requirement type='package' version="0.20.1">cython</requirement> </requirements> <description>learn fragment normalization values using probablistic approach</description>
--- a/hifive/hifive/learn_hic_normalization.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/learn_hic_normalization.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,9 +1,9 @@ <tool id="learn_hic_normalization" name="normalize_HiC_project"> <requirements> <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="1.7.1">numpy</requirement> + <requirement type='package' version="0.12.0">scipy</requirement> + <requirement type='package' version="2.5.0">h5py</requirement> <requirement type='package' version="0.20.1">cython</requirement> </requirements> <description>learn fend normalization values using probablistic approach</description>
--- a/hifive/hifive/tool_dependencies.xml Thu Apr 16 15:57:50 2015 -0400 +++ b/hifive/hifive/tool_dependencies.xml Thu Apr 16 16:35:12 2015 -0400 @@ -1,21 +1,18 @@ <?xml version="1.0"?> <tool_dependency> - <package name="scipy" version="0.12"> + <package name="scipy" version="0.12.0"> <repository changeset_revision="d607515b0510" name="package_scipy_0_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="numpy" version="1.7"> + <package name="numpy" version="1.7.1"> <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"/> </package> - <package name="h5py" version="2.4.0"> - <repository changeset_revision="79b31a4c757c" name="package_h5py_2_4_0" owner="sauria" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="h5py" version="2.5.0"> + <repository changeset_revision="cac2248ec1fd" name="package_h5py_2_5_0" owner="sauria" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="hifive" version="1.0.2"> - <repository changeset_revision="18a457921969" name="package_hifive_1_0_2" owner="sauria" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="1ce493f18c23" 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> - </set_environment> </tool_dependency>