From f196629c07c7a036fd0b77638165d3fbd479be5e Mon Sep 17 00:00:00 2001 From: Brian Haas Date: Sat, 14 Mar 2020 00:23:06 +0000 Subject: [PATCH] use ctat genome lib env var for makefile setting --- example/Makefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/example/Makefile b/example/Makefile index 802261b..fc1a048 100644 --- a/example/Makefile +++ b/example/Makefile @@ -18,10 +18,10 @@ TrinityFusion-UC: TrinityFusion-UC-Singularity: - singularity exec -e -B /home/bhaas/CTAT_GENOMICS/GRCh37_gencode_v19_CTAT_lib_Aug152019.plug-n-play/ctat_genome_lib_build_dir:/ctat_genome_lib:ro TrinityFusion.simg /usr/local/src/TrinityFusion/TrinityFusion --left_fq reads_1.fq.gz --right_fq reads_2.fq.gz --output_dir TrinityFusion-UC_outdir-Singularity --chimeric_junctions Chimeric.out.junction --aligned_bam Aligned.out.bam --genome_lib_dir /ctat_genome_lib + singularity exec -e -B ${CTAT_GENOME_LIB}:/ctat_genome_lib:ro TrinityFusion.simg /usr/local/src/TrinityFusion/TrinityFusion --left_fq reads_1.fq.gz --right_fq reads_2.fq.gz --output_dir TrinityFusion-UC_outdir-Singularity --chimeric_junctions Chimeric.out.junction --aligned_bam Aligned.out.bam --genome_lib_dir /ctat_genome_lib trinityFusion-UC-Docker: - docker run --rm -v `pwd`:/data -v /home/bhaas/CTAT_GENOMICS/GRCh37_gencode_v19_CTAT_lib_Aug152019.plug-n-play/ctat_genome_lib_build_dir:/ctat_genome_lib:ro trinityctat/trinityfusion /usr/local/src/TrinityFusion/TrinityFusion --left_fq /data/reads_1.fq.gz --right_fq /data/reads_2.fq.gz --output_dir /data/TrinityFusion-UC_outdir-Docker --chimeric_junctions /data/Chimeric.out.junction --aligned_bam /data/Aligned.out.bam --genome_lib_dir /ctat_genome_lib + docker run --rm -v `pwd`:/data -v ${CTAT_GENOME_LIB}:/ctat_genome_lib:ro trinityctat/trinityfusion /usr/local/src/TrinityFusion/TrinityFusion --left_fq /data/reads_1.fq.gz --right_fq /data/reads_2.fq.gz --output_dir /data/TrinityFusion-UC_outdir-Docker --chimeric_junctions /data/Chimeric.out.junction --aligned_bam /data/Aligned.out.bam --genome_lib_dir /ctat_genome_lib clean: