Repository data_manager_build_alfa_indexes
Owner: biocomp-ibens
Synopsis: Build ALFA indexes from automatically downloaded gtf annotation file
1. The tool asks the admin to enter a 'species_name' and automatically download the last release of the corresponding gtf annotation file on Ensembl. 
2. The tool calls ALFA to generate the alfa indexes from this gtf file.
3. Resulting indexes are stored in the child directory 'alfa_indexes' of the dir <galaxy_data_manager_data_path> defined in config/galaxy.ini
4. Finally, the tool adds the new entry to the table 'alfa_indexes.loc'. This .loc file is where the data table 'alfa_indexes' points, as defined in config/shed_tool_data_table.conf.xml
5. At the end of the process, when a user will use alfa (https://toolshed.g2.bx.psu.edu/view/charles-bernard/alfa), the built-in indexes corresponding to the 'species_name' will be available
Type: unrestricted
Revision: 0:f68a60c3d768
This revision can be installed: True
Times cloned / installed: 64
Dependencies of this repository

Repository package_ncurses_5_9 revision 335ebf512407 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_python_2_7_numpy_1_9 revision f24fc0b630fc owned by iuc (prior install required)
Repository package_freetype_2_5_2_matplotlib_fix revision 26586565bc22 owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 588666932a32 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_python_2_7_10 revision bd7165ea6526 owned by iuc (prior install required)
Repository package_atlas_3_10 revision 98c017ec230d owned by iuc (prior install required)
Repository package_python_2_7_10 revision bd7165ea6526 owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 588666932a32 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_readline_6_3 revision ca1a9400d4e1 owned by iuc (prior install required)
Repository package_bzlib_1_0 revision af4887e1f595 owned by iuc (prior install required)
Repository package_xz_5_0_5 revision 944f93d45594 owned by iuc (prior install required)
Repository package_sqlite_3_8_3 revision c8a5c11cc921 owned by iuc (prior install required)
Repository package_gdbm_1_11 revision ed2537bccffc owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_libtool_2_4 revision 7f67694b167c owned by iuc (prior install required)
Repository package_bedtools_2_24 revision 3416a1d4a582 owned by iuc (prior install required)

Name Version Type
bedtools 2.24 package
matplotlib 1.4 package
samtools 1.2 package

Contents of this repository

Name Description Version Minimum Galaxy Version
build ALFA indexes from automatically downloaded gtf annotation file 0.0.1 16.01

Name Version Data Tables
build_alfa_indexes 0.0.1 alfa_indexes

Categories
Data Managers - Utilities for Managing Galaxy's built-in data cache