Mercurial > repos > bgruening > deeptools

changeset 63:07513cab0338 draft

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Uploaded
author bgruening
date Thu, 26 Feb 2015 11:04:18 -0500
parents 1d932daaa198
children 627004611e98
files deepTools_macros.xml tool_dependencies.xml
diffstat 2 files changed, 4 insertions(+), 111 deletions(-) [+]
line wrap: on
line diff
--- a/deepTools_macros.xml	Tue Jan 27 15:19:23 2015 -0500
+++ b/deepTools_macros.xml	Thu Feb 26 11:04:18 2015 -0500
@@ -31,22 +31,12 @@
             help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000". (--region)" />
     </xml>
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">1.5.9.1</token>
+    <token name="@WRAPPER_VERSION@">1.5.9.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="binary">@BINARY@</requirement>
-            <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
-            <requirement type="package" >ucsc_tools</requirement>
-            <requirement type="package" version="2.7">python</requirement>
-            <requirement type="package" version="1.5.9.1">deepTools</requirement>
-            <requirement type="package" version="0.1">ucsc_tools</requirement>
-            <requirement type="package" version="1.9">numpy</requirement>
-            <requirement type="package" version="0.8.1">pysam</requirement>
-            <requirement type="package" version="0.14">scipy</requirement>
-            <requirement type="package" version="1.4">matplotlib</requirement>
-            <requirement type="package" version="0.1.19">samtools</requirement>
-            <requirement type="package" version="0.7.2">bx-python</requirement>
+            <requirement type="package" version="1.5.9">deepTools</requirement>
             <yield />
         </requirements>
         <version_command>@BINARY@ --version</version_command>
--- a/tool_dependencies.xml	Tue Jan 27 15:19:23 2015 -0500
+++ b/tool_dependencies.xml	Thu Feb 26 11:04:18 2015 -0500
@@ -1,103 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="samtools" version="0.1.19">
-        <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="numpy" version="1.9">
-        <repository changeset_revision="dd91d64330d4" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="matplotlib" version="1.4">
-        <repository changeset_revision="38e91928f905" name="package_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="scipy" version="0.14">
-        <repository changeset_revision="a257ce4d82ad" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="pysam" version="0.8.1">
-        <repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bx-python" version="0.7.2">
-        <repository changeset_revision="8c4879fee3cc" name="package_bx_python_0_7_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="python" version="2.7">
-        <repository changeset_revision="2c52c900e56a" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="deepTools" version="1.5.9">
+        <repository changeset_revision="ebb8126cb112" name="package_deeptools_1_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="ucsc_tools" version="0.1">
-        <install version="1.0">
-            <actions>
-                <action type="download_binary">
-                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
-                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
-                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
-                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
-                </action>
-                <action type="chmod">
-                    <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
-                </action>
-                <action type="download_binary">
-                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
-                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
-                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
-                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
-                </action>
-                <action type="chmod">
-                    <file mode="755">$INSTALL_DIR/bigWigInfo</file>
-                </action>
-                <action type="download_binary">
-                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph</url_template>
-                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
-                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
-                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph</url_template>
-                </action>
-                <action type="chmod">
-                    <file mode="755">$INSTALL_DIR/bigWigToBedGraph</file>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
-                </action>
-             </actions>
-         </install>
-         <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
-     </package>
-
-    <package name="deepTools" version="1.5.9.1">
-        <install version="1.0">
-            <actions>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="pysam" version="0.8.1" />
-                    </repository>
-                    <repository changeset_revision="8c4879fee3cc" name="package_bx_python_0_7_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="bx-python" version="0.7.2" />
-                    </repository>
-                    <repository changeset_revision="dd91d64330d4" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="numpy" version="1.9" />
-                    </repository>
-                    <repository changeset_revision="38e91928f905" name="package_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="matplotlib" version="1.4" />
-                    </repository>
-                    <repository changeset_revision="a257ce4d82ad" name="package_scipy_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="scipy" version="0.14" />
-                    </repository>
-                </action>
-                <action type="setup_python_environment">
-                   <repository changeset_revision="2c52c900e56a" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                       <package name="python" version="2.7" />
-                   </repository>
-                    <!-- allow downloading and installing an Python package from https://pypi.org/ -->
-                    <package>https://pypi.python.org/packages/source/d/deepTools/deepTools-1.5.9.1.tar.gz</package>
-                </action>
-
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
-                    <!-- disable the config file of deepTools -->
-                    <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
-                </action>
-             </actions>
-         </install>
-         <readme>
-            Installation of deepTools from Fidel Ramirez.
-            https://github.com/fidelram/deepTools
-         </readme>
-     </package>
 </tool_dependency>