[med-svn] [Git][med-team/trinityrnaseq][master] Don't hardcode number of --CPU (especially above 2)
Michael R. Crusoe
gitlab at salsa.debian.org
Fri Jan 4 14:02:37 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / trinityrnaseq
Commits:
5114b4da by Michael R. Crusoe at 2019-01-04T11:38:49Z
Don't hardcode number of --CPU (especially above 2)
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/unfix_num_of_cores
Changes:
=====================================
debian/changelog
=====================================
@@ -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 <michael.crusoe at gmail.com> 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.
=====================================
debian/control
=====================================
@@ -64,7 +64,8 @@ Architecture: all
Depends: ${perl:Depends},
${java:Depends},
${misc:Depends},
- r-base-core
+ r-base-core,
+ coreutils
Recommends: trinityrnaseq
Description: RNA-Seq De novo Assembly common example and testing files
Trinity represents a novel method for the efficient and robust de novo
=====================================
debian/patches/series
=====================================
@@ -13,3 +13,4 @@ disable-libieee
# assume_modern_g++.patch
python3
better_java_version_check
+unfix_num_of_cores
=====================================
debian/patches/unfix_num_of_cores
=====================================
@@ -0,0 +1,441 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Don't hardcode number of --CPU (especially above 2)
+
+blastn -num_threads will not accept a number larger than the cores/CPUs it
+detects and will exit with an error. Some Debian test (virtual) machines only
+have two cores and thus they failed our testing.
+
+With this patch we detect in a unix/macOS friendly way the number of cores
+using `nproc` or `sysctl -n hw.physicalcpu` (respectively). Thus execution of
+the sample_data tests will be much faster for most developers/users.
+
+Perhaps Trinity itself could be taught this trick and the --CPU option would
+not be needed by default.
+
+--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe.diff_kmer_length.sh
++++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe.diff_kmer_length.sh
+@@ -19,14 +19,14 @@
+ gunzip -c reads2.left.fq.gz > reads2.left.fq
+ fi
+
+-
++CPU=$(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 #####
+
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/commit/5114b4da2da34b28618012431ca6d288afd2f38e
--
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/commit/5114b4da2da34b28618012431ca6d288afd2f38e
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