use ctat genome lib env var for makefile setting

trinityrnaseq · Mar 14, 2020 · f196629 · f196629
1 parent b329f71
commit f196629
Showing 1 changed file with 2 additions and 2 deletions.
diff --git 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: