From bf38d40209ad79144e1106b5bd063d94b442b81a Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Thu, 15 Sep 2016 12:31:30 +0200 Subject: [PATCH 1/3] Add package_fastx_toolkit_0_0_14 --- .../package_fastx_toolkit_0_0_14/.shed.yml | 8 ++++++ .../tool_dependencies.xml | 26 +++++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 packages/package_fastx_toolkit_0_0_14/.shed.yml create mode 100644 packages/package_fastx_toolkit_0_0_14/tool_dependencies.xml diff --git a/packages/package_fastx_toolkit_0_0_14/.shed.yml b/packages/package_fastx_toolkit_0_0_14/.shed.yml new file mode 100644 index 00000000000..33bb8270b96 --- /dev/null +++ b/packages/package_fastx_toolkit_0_0_14/.shed.yml @@ -0,0 +1,8 @@ +categories: +- Tool Dependency Packages +description: Contains a tool dependency definition that downloads and compiles version + 0.0.14 of the fastx toolkit. +name: package_fastx_toolkit_0_0_14 +owner: iuc +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_fastx_toolkit_0_0_14 +type: tool_dependency_definition diff --git a/packages/package_fastx_toolkit_0_0_14/tool_dependencies.xml b/packages/package_fastx_toolkit_0_0_14/tool_dependencies.xml new file mode 100644 index 00000000000..99982556eb3 --- /dev/null +++ b/packages/package_fastx_toolkit_0_0_14/tool_dependencies.xml @@ -0,0 +1,26 @@ + + + + + + + + + + https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2 + + + + + + ./configure --prefix=$INSTALL_DIR --disable-wall + make && make install + + + $INSTALL_DIR/bin + + + + + + From 231157132a50f5bc8f9d0c8151c4ddca86c97213 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Thu, 15 Sep 2016 12:37:49 +0200 Subject: [PATCH 2/3] Remove unused tags --- .../tool_dependencies.xml | 36 +++++++++---------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/packages/package_fastx_toolkit_0_0_14/tool_dependencies.xml b/packages/package_fastx_toolkit_0_0_14/tool_dependencies.xml index 99982556eb3..7898f68b17a 100644 --- a/packages/package_fastx_toolkit_0_0_14/tool_dependencies.xml +++ b/packages/package_fastx_toolkit_0_0_14/tool_dependencies.xml @@ -1,26 +1,26 @@ + + + - - - - - - https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2 - - - - - - ./configure --prefix=$INSTALL_DIR --disable-wall - make && make install - - - $INSTALL_DIR/bin + + https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2 + + + + - + ./configure --prefix=$INSTALL_DIR --disable-wall + make && make install + + + $INSTALL_DIR/bin + - + + The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. + From 2651db48026cd713d19eba168e63712b1466984f Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Thu, 15 Sep 2016 14:16:14 +0200 Subject: [PATCH 3/3] package_fastx_toolkit_0_0_14 also needs an update of package_libgtextutils --- .../tool_dependencies.xml | 45 ++++++++++++------- packages/package_libgtextutils_0_7/.shed.yml | 8 ++++ .../tool_dependencies.xml | 17 +++++++ 3 files changed, 55 insertions(+), 15 deletions(-) create mode 100644 packages/package_libgtextutils_0_7/.shed.yml create mode 100644 packages/package_libgtextutils_0_7/tool_dependencies.xml diff --git a/packages/package_fastx_toolkit_0_0_14/tool_dependencies.xml b/packages/package_fastx_toolkit_0_0_14/tool_dependencies.xml index 7898f68b17a..6b8fafae934 100644 --- a/packages/package_fastx_toolkit_0_0_14/tool_dependencies.xml +++ b/packages/package_fastx_toolkit_0_0_14/tool_dependencies.xml @@ -1,23 +1,38 @@ - - + + - - https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2 - - - - - - ./configure --prefix=$INSTALL_DIR --disable-wall - make && make install - - - $INSTALL_DIR/bin - + + + https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2 + + + + + + + + $INSTALL_DIR/bin + + + + https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2 + + + + + + --disable-wall + + $INSTALL_DIR/bin + + + The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. diff --git a/packages/package_libgtextutils_0_7/.shed.yml b/packages/package_libgtextutils_0_7/.shed.yml new file mode 100644 index 00000000000..59ecef069c6 --- /dev/null +++ b/packages/package_libgtextutils_0_7/.shed.yml @@ -0,0 +1,8 @@ +categories: +- Tool Dependency Packages +description: Contains a tool dependency definition that downloads and compiles version + 0.7 of the gtextutils libraries. +name: package_libgtextutils_0_7 +owner: iuc +remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_libgtextutils_0_7 +type: tool_dependency_definition diff --git a/packages/package_libgtextutils_0_7/tool_dependencies.xml b/packages/package_libgtextutils_0_7/tool_dependencies.xml new file mode 100644 index 00000000000..d05c14a4e5d --- /dev/null +++ b/packages/package_libgtextutils_0_7/tool_dependencies.xml @@ -0,0 +1,17 @@ + + + + + + https://github.com/agordon/libgtextutils/releases/download/0.7/libgtextutils-0.7.tar.gz + + --disable-wall + + $INSTALL_DIR/lib/pkgconfig + + + + + + +