diff -Nru trinityrnaseq-2.6.6+dfsg/debian/changelog trinityrnaseq-2.6.6+dfsg/debian/changelog --- trinityrnaseq-2.6.6+dfsg/debian/changelog 2019-01-03 09:15:29.000000000 +0000 +++ trinityrnaseq-2.6.6+dfsg/debian/changelog 2019-01-04 11:38:40.000000000 +0000 @@ -1,3 +1,11 @@ +trinityrnaseq (2.6.6+dfsg-6) unstable; urgency=medium + + * -examples: Don't hardcode number of --CPU (especially above 2). Fixes the + autopkgtests when the number of CPUs/cores is less than 4 and blastn's + intransigency to accept a larger value to -num_threads. + + -- Michael R. Crusoe Fri, 04 Jan 2019 03:38:40 -0800 + trinityrnaseq (2.6.6+dfsg-5) unstable; urgency=medium * Added missing dependency on ncbi-blast+ to the binary package. diff -Nru trinityrnaseq-2.6.6+dfsg/debian/control trinityrnaseq-2.6.6+dfsg/debian/control --- trinityrnaseq-2.6.6+dfsg/debian/control 2019-01-03 09:14:20.000000000 +0000 +++ trinityrnaseq-2.6.6+dfsg/debian/control 2019-01-03 15:51:23.000000000 +0000 @@ -64,7 +64,8 @@ Depends: ${perl:Depends}, ${java:Depends}, ${misc:Depends}, - r-base-core + r-base-core, + coreutils Recommends: trinityrnaseq Description: RNA-Seq De novo Assembly common example and testing files Trinity represents a novel method for the efficient and robust de novo diff -Nru trinityrnaseq-2.6.6+dfsg/debian/patches/series trinityrnaseq-2.6.6+dfsg/debian/patches/series --- trinityrnaseq-2.6.6+dfsg/debian/patches/series 2019-01-02 08:13:18.000000000 +0000 +++ trinityrnaseq-2.6.6+dfsg/debian/patches/series 2019-01-03 15:29:42.000000000 +0000 @@ -13,3 +13,4 @@ # assume_modern_g++.patch python3 better_java_version_check +unfix_num_of_cores diff -Nru trinityrnaseq-2.6.6+dfsg/debian/patches/unfix_num_of_cores trinityrnaseq-2.6.6+dfsg/debian/patches/unfix_num_of_cores --- trinityrnaseq-2.6.6+dfsg/debian/patches/unfix_num_of_cores 1970-01-01 00:00:00.000000000 +0000 +++ trinityrnaseq-2.6.6+dfsg/debian/patches/unfix_num_of_cores 2019-01-03 15:48:01.000000000 +0000 @@ -0,0 +1,441 @@ +From: Michael R. Crusoe +Subject: Don't hardcode number of --CPU (especially above 2) + +blastn -num_threads will not accept a number larger than the cores/CPUs it +detects and will exit with an error. Some Debian test (virtual) machines only +have two cores and thus they failed our testing. + +With this patch we detect in a unix/macOS friendly way the number of cores +using `nproc` or `sysctl -n hw.physicalcpu` (respectively). Thus execution of +the sample_data tests will be much faster for most developers/users. + +Perhaps Trinity itself could be taught this trick and the --CPU option would +not be needed by default. + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe.diff_kmer_length.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe.diff_kmer_length.sh +@@ -19,14 +19,14 @@ + gunzip -c reads2.left.fq.gz > reads2.left.fq + fi + +- ++CPU=$(nproc || sysctl -n hw.physicalcpu) + + ####################################################### + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + + ## use jellyfish +-../../Trinity --seqType fq --JM 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4 --trimmomatic --normalize_reads --no_cleanup --KMER_SIZE $KMER_SIZE ++../../Trinity --seqType fq --JM 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU ${CPU} --trimmomatic --normalize_reads --no_cleanup --KMER_SIZE $KMER_SIZE + + ##### Done Running Trinity ##### + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_CuffFly.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_CuffFly.sh +@@ -9,14 +9,14 @@ + gunzip -c reads.left.fq.gz > reads.left.fq + fi + +- ++CPU=$(nproc || sysctl -n hw.physicalcpu) + + ####################################################### + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + + ## use jellyfish +-../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --CuffFly ++../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU ${CPU} --CuffFly + + ##### Done Running Trinity ##### + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_PasaFly.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_PasaFly.sh +@@ -9,14 +9,14 @@ + gunzip -c reads.left.fq.gz > reads.left.fq + fi + +- ++CPU=$(nproc || sysctl -n hw.physicalcpu) + + ####################################################### + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + + ## use jellyfish +-../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --PasaFly ++../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU ${CPU} --PasaFly + + ##### Done Running Trinity ##### + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_as_DS.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_as_DS.sh +@@ -4,8 +4,10 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ## use jellyfish +-../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU 4 ++../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU ${CPU} + + ##### Done Running Trinity ##### + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_bowtie_components.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_bowtie_components.sh +@@ -9,14 +9,14 @@ + gunzip -c reads.left.fq.gz > reads.left.fq + fi + +- ++CPU=$(nproc || sysctl -n hw.physicalcpu) + + ####################################################### + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + + ## use jellyfish +-../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --bowtie_comp ++../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU ${CPU} --bowtie_comp + + ##### Done Running Trinity ##### + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_full_cleanup.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_full_cleanup.sh +@@ -4,8 +4,10 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ## use jellyfish +-../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 2 --full_cleanup ++../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU ${CPU} --full_cleanup + + ##### Done Running Trinity ##### + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_include_long_reads.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_include_long_reads.sh +@@ -4,13 +4,15 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ## use jellyfish + ../../Trinity --seqType fq \ + --max_memory 2G \ + --left reads.left.fq.gz \ + --right reads.right.fq.gz \ + --SS_lib_type RF \ +- --CPU 4 \ ++ --CPU ${CPU} \ + --no_cleanup \ + --long_reads longReads.fa \ + --output test_trinity_long_reads +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_cleanup.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_cleanup.sh +@@ -4,8 +4,10 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ## use jellyfish +-../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 2 --no_cleanup ++../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU ${CPU} --no_cleanup + + ##### Done Running Trinity ##### + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_parallel_iworm_assembly.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_parallel_iworm_assembly.sh +@@ -9,14 +9,14 @@ + gunzip -c reads.left.fq.gz > reads.left.fq + fi + +- ++CPU=$(nproc || sysctl -n hw.physicalcpu) + + ####################################################### + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + + ## use jellyfish +-../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --PARALLEL_IWORM ++../../Trinity.pl --seqType fq --JM 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU ${CPU} --PARALLEL_IWORM + + ##### Done Running Trinity ##### + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_piecemeal.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_piecemeal.sh +@@ -4,17 +4,19 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + # stop before inchworm (just in silico norm) +-../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU 4 --output trinity_piecemeal --no_run_inchworm ++../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU ${CPU} --output trinity_piecemeal --no_run_inchworm + + # stop before chrysalis +-../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU 4 --output trinity_piecemeal --no_run_chrysalis ++../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU ${CPU} --output trinity_piecemeal --no_run_chrysalis + + # stop before phase 2 +-../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU 4 --output trinity_piecemeal --no_distributed_trinity_exec ++../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU ${CPU} --output trinity_piecemeal --no_distributed_trinity_exec + + # finish it up +-../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU 4 --output trinity_piecemeal ++../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU ${CPU} --output trinity_piecemeal + + + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_trin_complete.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_trin_complete.sh +@@ -4,10 +4,12 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ../../Trinity --seqType fq --max_memory 2G \ + --left reads.left.fq.gz \ + --right reads.right.fq.gz \ + --SS_lib_type RF \ +- --CPU 4 --trinity_complete --no_cleanup --output trinity_complete ++ --CPU ${CPU} --trinity_complete --no_cleanup --output trinity_complete + + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_bowtie2.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_bowtie2.sh +@@ -4,6 +4,8 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ## use jellyfish + ../../Trinity \ + --seqType fq \ +@@ -11,7 +13,7 @@ + --left reads.left.fq.gz \ + --right reads.right.fq.gz \ + --SS_lib_type RF \ +- --CPU 4 \ ++ --CPU ${CPU} \ + --no_cleanup \ + --use_bowtie2 \ + --output test_trinity_bowtie2 +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_my_ramdisk.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_my_ramdisk.sh +@@ -15,11 +15,13 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ../../Trinity --seqType fq --max_memory 2G \ + --left reads.left.fq \ + --right reads.right.fq \ + --SS_lib_type RF \ +- --CPU 4 \ ++ --CPU ${CPU} \ + --workdir /Volumes/RamDisk/trinity.workdir.$$ --full_cleanup + + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_workdir.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_workdir.sh +@@ -15,11 +15,13 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ../../Trinity --seqType fq --max_memory 2G \ + --left reads.left.fq \ + --right reads.right.fq \ + --SS_lib_type RF \ +- --CPU 4 \ ++ --CPU ${CPU} \ + --output trinity_with_workdir \ + --workdir /tmp/trinity.workdir.$$ --full_cleanup + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_using_Grid_LSF.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_using_Grid_LSF.sh +@@ -4,8 +4,6 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + +- +- +-../../Trinity --seqType fq --JM 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 4 --grid_conf_file ../../htc_conf/BroadInst_LSF.test.conf ++../../Trinity --seqType fq --JM 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU $4 --grid_conf_file ../../htc_conf/BroadInst_LSF.test.conf + + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_w_monitoring.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_w_monitoring.sh +@@ -15,6 +15,8 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + # monitoring at 1 second intervals because this test runs very quick. You might monitor on the order of minutes rather than seconds for 'regular' runs. +-../../Trinity --seqType fq --max_memory 1G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --monitoring --monitor_sec 1 --output trinity_out_dir_monitored ++../../Trinity --seqType fq --max_memory 1G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU ${CPU} --monitoring --monitor_sec 1 --output trinity_out_dir_monitored + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming.sh +@@ -15,6 +15,8 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ## use jellyfish + ../../Trinity \ + --seqType fq \ +@@ -22,7 +24,7 @@ + --left reads.left.fq \ + --right reads.right.fq \ + --SS_lib_type RF \ +- --CPU 4 \ ++ --CPU ${CPU} \ + --no_normalize_reads \ + --trimmomatic \ + --output __test_trinity_with_trimmomatic +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh +@@ -15,8 +15,10 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ## use jellyfish +-../../Trinity --seqType fq --max_memory 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --trimmomatic --normalize_reads --output __test_trinity_qual_and_norm ++../../Trinity --seqType fq --max_memory 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU ${CPU} --trimmomatic --normalize_reads --output __test_trinity_qual_and_norm + + ##### Done Running Trinity ##### + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh +@@ -22,13 +22,15 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ## use jellyfish + ../../Trinity --seqType fq \ + --max_memory 2G \ + --left reads.left.fq,reads2.left.fq \ + --right reads.right.fq,reads2.right.fq \ + --SS_lib_type RF \ +- --CPU 4 \ ++ --CPU ${CPU} \ + --trimmomatic \ + --normalize_reads \ + --normalize_by_read_set \ +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe.singleFQ.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe.singleFQ.sh +@@ -6,7 +6,9 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + +-../../Trinity.pl --seqType fq --single reads.left.fq.gz --JM 1G --CPU 4 --output trinity_single_outdir ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ ++../../Trinity.pl --seqType fq --single reads.left.fq.gz --JM 1G --CPU {CPU} --output trinity_single_outdir + + + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_NO_normalization.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_NO_normalization.sh +@@ -15,13 +15,15 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ## use jellyfish + ../../Trinity --seqType fq \ + --max_memory 2G \ + --left reads.left.fq \ + --right reads.right.fq \ + --SS_lib_type RF \ +- --CPU 4 \ ++ --CPU ${CPU} \ + --no_normalize_reads \ + --output __test_trinity_wo_normalization + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_docker.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_docker.sh +@@ -1,2 +1,4 @@ +-docker run --rm -v`pwd`:`pwd` trinityrnaseq/trinityrnaseq Trinity --seqType fq --single `pwd`/reads.left.fq.gz --max_memory 1G --CPU 2 --output `pwd`/trinity_out_dir_docker ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ ++docker run --rm -v`pwd`:`pwd` trinityrnaseq/trinityrnaseq Trinity --seqType fq --single `pwd`/reads.left.fq.gz --max_memory 1G --CPU ${CPU} --output `pwd`/trinity_out_dir_docker + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_include_normalization.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_include_normalization.sh +@@ -15,8 +15,10 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ## use jellyfish +-../../Trinity --seqType fq --max_memory 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --normalize_reads --output __test_trinity_w_normalization ++../../Trinity --seqType fq --max_memory 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU ${CPU} --normalize_reads --output __test_trinity_w_normalization + + ##### Done Running Trinity ##### + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_lenient_path_extension.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_lenient_path_extension.sh +@@ -15,7 +15,9 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ## use jellyfish +-../../Trinity --seqType fq --max_memory 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --path_reinforcement_distance 1 --output __test_trinity_lenient_path_ext ++../../Trinity --seqType fq --max_memory 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU ${CPU} --path_reinforcement_distance 1 --output __test_trinity_lenient_path_ext + + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/runMe_no_qualTrim.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/runMe_no_qualTrim.sh +@@ -6,8 +6,10 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ## use jellyfish +-../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4 --normalize_reads --no_cleanup --output trinity_test_no_qtrim ++../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU ${CPU} --normalize_reads --no_cleanup --output trinity_test_no_qtrim + + ##### Done Running Trinity ##### + +--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/runMe.sh ++++ trinityrnaseq/sample_data/test_Trinity_Assembly/runMe.sh +@@ -4,11 +4,13 @@ + ## Run Trinity to Generate Transcriptome Assemblies ## + ####################################################### + ++CPU=$(nproc || sysctl -n hw.physicalcpu) ++ + ../../Trinity --seqType fq --max_memory 2G \ + --left reads.left.fq.gz \ + --right reads.right.fq.gz \ + --SS_lib_type RF \ +- --CPU 4 ++ --CPU ${CPU} + + ##### Done Running Trinity ##### +