# HG changeset patch # User iuc # Date 1459247626 14400 # Node ID 987ca85aead4c7915e5c516f674304a9a546e770 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rsem_1_2_28 commit 3c4a2b13b0f3a280de4f98f4f5e0dc29e10fc7a0 diff -r 000000000000 -r 987ca85aead4 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Mar 29 06:33:46 2016 -0400 @@ -0,0 +1,142 @@ + + + + + + + + + + + + + https://github.com/deweylab/RSEM/archive/v1.2.28.tar.gz + + + + + + + + + + sed -i.bak -e 's/-lcurses/-lncurses/' samtools*/Makefile samtools*/config.mk + sed -i.bak -e "s|-lz|-lz -L${ZLIB_ROOT_PATH}/lib|" Makefile samtools*/Makefile + make + + + rsem-bam2readdepth + $INSTALL_DIR + + + rsem-bam2wig + $INSTALL_DIR + + + rsem-build-read-index + $INSTALL_DIR + + + rsem-calculate-credibility-intervals + $INSTALL_DIR + + + rsem-calculate-expression + $INSTALL_DIR + + + rsem-control-fdr + $INSTALL_DIR + + + rsem-extract-reference-transcripts + $INSTALL_DIR + + + rsem-gen-transcript-plots + $INSTALL_DIR + + + rsem-generate-data-matrix + $INSTALL_DIR + + + rsem-generate-ngvector + $INSTALL_DIR + + + rsem-get-unique + $INSTALL_DIR + + + rsem-gff3-to-gtf + $INSTALL_DIR + + + rsem-parse-alignments + $INSTALL_DIR + + + rsem-plot-model + $INSTALL_DIR + + + rsem-plot-transcript-wiggles + $INSTALL_DIR + + + rsem-prepare-reference + $INSTALL_DIR + + + rsem-preref + $INSTALL_DIR + + + rsem-refseq-extract-primary-assembly + $INSTALL_DIR + + + rsem-run-ebseq + $INSTALL_DIR + + + rsem-run-em + $INSTALL_DIR + + + rsem-run-gibbs + $INSTALL_DIR + + + rsem-sam-validator + $INSTALL_DIR + + + rsem-scan-for-paired-end-reads + $INSTALL_DIR + + + rsem-simulate-reads + $INSTALL_DIR + + + rsem-synthesis-reference-transcripts + $INSTALL_DIR + + + rsem-tbam2gbam + $INSTALL_DIR + + + rsem_perl_utils.pm + $INSTALL_DIR + + + + $INSTALL_DIR/ + + + + +