Mercurial > repos > iuc > package_sra_toolkit_2_6_2

changeset 0:98414d1f9480 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_6_2 commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
author iuc
date Tue, 17 May 2016 14:14:22 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 63 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 17 14:14:22 2016 -0400
@@ -0,0 +1,63 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="perl" version="5.18.1">
+        <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="libmagic" version="5.25">
+        <repository changeset_revision="21b08f55a6ac" name="package_libmagic_5_25" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ncbi_vdb" version="2.6.2">
+        <repository changeset_revision="be38d36c735d" name="package_ncbi_vdb_2_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ngs_sdk" version="1.2.3">
+        <repository changeset_revision="3da0f4d34e92" name="package_ngs_sdk_1_2_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="sra_toolkit" version="2.6.2">
+        <install version="1.0">
+            <actions>
+                <action sha256sum="7aa1ec118486cd877bf2976818a3f319674584f3d04931a6ce2a92f6a9defbc1" type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.6.2.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="perl" version="5.18.1" />
+                    </repository>
+                    <repository changeset_revision="21b08f55a6ac" name="package_libmagic_5_25" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="libmagic" version="5.25" />
+                    </repository>
+                    <repository changeset_revision="be38d36c735d" name="package_ncbi_vdb_2_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="ncbi_vdb" version="2.6.2" />
+                    </repository>
+                    <repository changeset_revision="3da0f4d34e92" name="package_ngs_sdk_1_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="ngs_sdk" version="1.2.3" />
+                    </repository>
+                </action>
+                <action type="shell_command">
+                    ./configure --prefix=$INSTALL_DIR -with-ngs-sdk-prefix=$NGS_SDK_DIR --with-ncbi-vdb-sources=$NCBI_VDB_DIR --with-ncbi-vdb-build=$NCBI_VDB_DIR --build=$INSTALL_DIR
+                </action>
+                <action type="make_install" />
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
+            This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
+            When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a
+            download of a large SRA data set.
+
+            Build Requirements:
+            - make
+            - git
+            - gcc
+            - g++
+            - libxml2
+            - libcurl4
+            - zlib
+
+            On a debian based Linux OS use:
+
+            apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
+
+        </readme>
+    </package>
+</tool_dependency>