Mercurial > repos > nick > dunovo
comparison tool_dependencies.xml @ 23:04a9c9e8c8c3 draft
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fd1625359a101d8a6b0b8d97028cc8be509398f2\n'-dirty
| author | nick |
|---|---|
| date | Fri, 05 Jan 2018 03:12:52 -0500 |
| parents | e875e5572808 |
| children | 4f1eb9bd336d |
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| 22:e875e5572808 | 23:04a9c9e8c8c3 |
|---|---|
| 17 <action type="shell_command">rmdir kalign utillib ET</action> | 17 <action type="shell_command">rmdir kalign utillib ET</action> |
| 18 <!-- download the utillib submodule --> | 18 <!-- download the utillib submodule --> |
| 19 <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action> | 19 <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action> |
| 20 <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action> | 20 <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action> |
| 21 <action type="shell_command">rm v0.1.0.tar.gz</action> | 21 <action type="shell_command">rm v0.1.0.tar.gz</action> |
| 22 <action type="shell_command">ls -lFhAb > /home/me/tmp/galaxy/install.root1.log</action> | 22 <action type="shell_command">ls -lFhAb > /home/me/tmp/galaxy/install.ls1.log</action> |
| 23 <action type="shell_command">ls -lFhAb utillib-0.1.0 > /home/me/tmp/galaxy/install.utillib1.log</action> | 23 <action type="shell_command">ls -lFhAb utillib-0.1.0 > /home/me/tmp/galaxy/install.ls2.log</action> |
| 24 <action type="shell_command">echo DEBUG $TMP_WORK_DIR</action> | |
| 24 <action rename_to="utillib" type="move_file"> | 25 <action rename_to="utillib" type="move_file"> |
| 25 <source>utillib-0.1.0</source> | 26 <source>utillib-0.1.0</source> |
| 26 <destination>.</destination> | 27 <destination>$TMP_WORK_DIR</destination> |
| 27 </action> | 28 </action> |
| 28 <action type="shell_command">ls -lFhAb > /home/me/tmp/galaxy/install.root2.log</action> | 29 <action type="shell_command">ls -lFhAb > /home/me/tmp/galaxy/install.ls3.log</action> |
| 29 <action type="shell_command">ls -lFhAb utillib-0.1.0 > /home/me/tmp/galaxy/install.utillib2.log</action> | 30 <action type="shell_command">ls -lFhAb utillib > /home/me/tmp/galaxy/install.ls4.log</action> |
| 30 <action type="shell_command">ls -lFhAb utillib > /home/me/tmp/galaxy/install.utillib3.log</action> | |
| 31 <!-- download the kalign submodule --> | 31 <!-- download the kalign submodule --> |
| 32 <action type="download_file">https://github.com/makrutenko/kalign-dunovo/archive/v0.2.0.tar.gz</action> | 32 <action type="download_file">https://github.com/makrutenko/kalign-dunovo/archive/v0.2.0.tar.gz</action> |
| 33 <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action> | 33 <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action> |
| 34 <action type="shell_command">rm v0.2.0.tar.gz</action> | 34 <action type="shell_command">rm v0.2.0.tar.gz</action> |
| 35 <action rename_to="kalign" type="move_file"> | 35 <action rename_to="kalign" type="move_file"> |
| 36 <source>kalign-dunovo-0.2.0</source> | 36 <source>kalign-dunovo-0.2.0</source> |
| 37 <destination>.</destination> | 37 <destination>$TMP_WORK_DIR</destination> |
| 38 </action> | 38 </action> |
| 39 <!-- download the ET submodule --> | 39 <!-- download the ET submodule --> |
| 40 <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action> | 40 <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action> |
| 41 <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action> | 41 <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action> |
| 42 <action type="shell_command">rm v0.2.2.tar.gz</action> | 42 <action type="shell_command">rm v0.2.2.tar.gz</action> |
| 43 <action rename_to="ET" type="move_file"> | 43 <action rename_to="ET" type="move_file"> |
| 44 <source>ET-0.2.2</source> | 44 <source>ET-0.2.2</source> |
| 45 <destination>.</destination> | 45 <destination>$TMP_WORK_DIR</destination> |
| 46 </action> | 46 </action> |
| 47 <!-- make and install --> | 47 <!-- make and install --> |
| 48 <action type="shell_command">make clean</action> | 48 <action type="shell_command">make clean</action> |
| 49 <action type="shell_command">make</action> | 49 <action type="shell_command">make</action> |
| 50 <action type="shell_command">ls -lFhAb > /home/me/tmp/galaxy/install.root4.log</action> | 50 <action type="shell_command">ls -lFhAb > /home/me/tmp/galaxy/install.ls5.log</action> |
| 51 <action type="move_directory_files"> | 51 <action type="move_directory_files"> |
| 52 <source_directory>.</source_directory> | 52 <source_directory>.</source_directory> |
| 53 <destination_directory>$INSTALL_DIR</destination_directory> | 53 <destination_directory>$INSTALL_DIR</destination_directory> |
| 54 </action> | 54 </action> |
| 55 <action type="shell_command">ls -lFhAb $INSTALL_DIR > /home/me/tmp/galaxy/install.install_dir1.log</action> | 55 <action type="shell_command">ls -lFhAb $INSTALL_DIR > /home/me/tmp/galaxy/install.ls6.log</action> |
| 56 <action type="set_environment"> | 56 <action type="set_environment"> |
| 57 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> | 57 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> |
| 58 </action> | 58 </action> |
| 59 </actions> | 59 </actions> |
| 60 </install> | 60 </install> |