Remove installation of problematic packages from ngs pipeline installation. chapmanb/bcbio-nextgen#58 chapmanb/bcbio-nextgen#56
Provide a generalized download process that tries both S3 and standard genome indexing for failure handling when download not available. Additional testing for deployment methods supporting bcbio-nextgen
Provide a minimal ngs_pipeline flavor with less requirements. Allows bcbio-nextgen pipeline installation with less external dependencies
Ensure CloudBioLinux PATH takes preference in .bashrc tweaking so updated programs will get called first when we need more recent versions
Avoid overwriting python_version_ext or ruby_version_ext if pre-set in fabricrc.txt. chapmanb/bcbio-nextgen#58
Improve data installation and Galaxy integration for local installs. Safely install on localhost with no ssh-setup for data. Create novoalign indexes equivalents and add to default tool_data_table_conf. chapmanb/bcbio-nextgen#63
Move debian package installation and additional custom packages to use local installation targets. This allows a minimal build of bcbio-nextgen on a localhost without ssh requirement, so nearly full support for local builds now
Support localhost non-ssh installation on RPM based CentOS and Scientific Linux sytems
Remove debugging code
Include LD_LIBRARY_PATH update to .bashrc for non-root installs. Enables bamtools binary which requires shared libraries
Ensure uniform usage of .bashrc by local/ssh scripts. Add LD_LIBRARY_PATH to .bashrc and checks for executables when non-standard install paths used
Avoid making sudo commands interactive: bad idea
Fix typo in checking for third party tool installation with locally updated LD_LIBRARY_PATH. Fixes chapmanb/bcbio-nextgen#73
Provide fixes for tricky sudo cases: download UCSC tools in temp directory and copy over. Fixes chapmanb/bcbio-nextgen#74 Copy installed binaries instead of move to avoid local permissions issues
Use copy to samtools installation to avoid issues where sudo has no write access to tmpdir
Include missing put command for non-local cloudbiolinux installations. Thanks to Zhi-Wei Lu