Reintegrate with Bam Bin Counting and Minor Change to GPL16043.sh #2
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…with just the make command. I also removed the redundant warning gcc flags (-Wall stands for warn all, and I confirmed that -Wall included all the other warnings).
Conflicts: makefile
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Reintegrate with Bam Bin Counting and Minor Change to GPL16043.sh
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I think I did the pull request right. There were some conflicts with my branch so I committed all the necessary changes that I could and then approved the merge pull request from the website. Then I ran git fetch origin Does that seem about right? Git confusing! |
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The pull request was automatically merged in github by pressing the big "Merge pull request" button (shown below), right? Generally you shouldn't need to run "git reset --hard origin/master". That is a dangerous command because it can overwrite your unsaved files. You can read more about that here: http://git-scm.com/blog I agree git is pretty confusing. I'll update the [https://github.com/BradnerLab/pipeline/wiki/Collaboration-Workflow](collaboration workflow page) to document an example of handling a conflict in a working directory after a merge. |
Motif multithread fasta input, 8x speedup with 8 core machine On deathstar with 8 physical cores (16 with hyperthreading), merging this branch speeds up fasta input / fimo output by 8x. Scales pretty well, but doesn't actually scale linearly; other optimizations allow using just a single thread on this branch to be 1.4x faster than before. Since we were already 8.3x faster than fimo, we should now be 66x faster than fimo on deathstar. See notes at https://docs.google.com/spreadsheets/d/1H9ZY6HLPY1qKIiIbbld9Pz05N0eFyY1nsoK42XWtR4g/edit#gid=1133261856
#1 "Sequence Data File Hot Spot Analysis"
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)