BradnerLab/pipeline — pull request #2 by jdimatteo (2013-12-17 07:22:21+00:00)
Title: Reintegrate with Bam Bin Counting and Minor Change to GPL16043.sh

GPL16043.sh - modified to use local copy of GPL16043.r (which is useful for Jenkins to run the copy of GPL16043.r that it cloned from github)
bam_liquidator_bin_count_tables.sql - creates mysql tables used by bin counting scripts
bam_liquidator_bin_counter.sh - populates counts mysql table with (unnormalized) bin counts -- can be run with Jenkins job Bam_Liquidator_Bin_Counter
bam_liquidator_bin_plot_by_cell_type.py - populates normalized bin counts with percentiles per bin for each cell_type
bamliquidator.c - updated to exit with non-zero return code when error encountered
bamliquidator.o - removed binary file (usually binary files aren't committed to git)
bamliquidator_make.sh
makefile - renamed from bamliquidator_make.sh, now a make file, so that you can just run "make" in the current directory to build it, which is customary for building C applications, also removed redundant gcc flags ("-Wall" stands for warn all, so it isn't necessary to list additional categories to give warnings about)
utils.pyc - removed binary file (usually binary files aren't committed to git)