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|
From: Michael R. Crusoe <michael.crusoe@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 ${CPU} --full_cleanup
##### Done Running Trinity #####
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_include_long_reads.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_include_long_reads.sh
@@ -4,13 +4,14 @@
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
+CPU=$(nproc || sysctl -n hw.physicalcpu)
${TRINITY_HOME}/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)
-${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU 4 --output trinity_piecemeal --no_run_inchworm
+${TRINITY_HOME}/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_HOME}/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_HOME}/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_HOME}/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_HOME}/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_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --CPU 4 --output trinity_piecemeal
+${TRINITY_HOME}/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.$$ --full_cleanup
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_workdir.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_workdir.sh
@@ -15,11 +15,13 @@
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
+CPU=$(nproc || sysctl -n hw.physicalcpu)
+
${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
--left reads.left.fq \
--right reads.right.fq \
--SS_lib_type RF \
- --CPU 4 \
+ --CPU ${CPU}\
--output trinity_with_workdir \
--workdir /tmp/trinity.workdir.$$ --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 ${CPU} --monitoring --monitor_sec 1 --output trinity_out_dir_monitored
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming.sh
@@ -15,6 +15,7 @@
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
+CPU=$(nproc || sysctl -n hw.physicalcpu)
${TRINITY_HOME}/Trinity \
--seqType fq \
@@ -22,7 +23,7 @@
--left reads.left.fq \
--right reads.right.fq \
--SS_lib_type RF \
- --CPU 4 \
+ --CPU ${CPU} \
--no_normalize_reads \
--trimmomatic \
--output __test_trinity_with_trimmomatic
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh
@@ -15,8 +15,9 @@
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
+CPU=$(nproc || sysctl -n hw.physicalcpu)
-${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU 4 --trimmomatic --normalize_reads --output __test_trinity_qual_and_norm
+${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq --right reads.right.fq --SS_lib_type RF --CPU ${CPU} --trimmomatic --normalize_reads --output __test_trinity_qual_and_norm
##### Done Running Trinity #####
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh
@@ -22,13 +22,14 @@
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
+CPU=$(nproc || sysctl -n hw.physicalcpu)
${TRINITY_HOME}/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_HOME}/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 ${CPU} --normalize_reads --no_cleanup --output trinity_test_no_qtrim
##### Done Running Trinity #####
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/runMe.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/runMe.sh
@@ -9,12 +9,13 @@
exit 1
fi
+CPU=$(nproc || sysctl -n hw.physicalcpu)
${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
--left reads.left.fq.gz \
--right reads.right.fq.gz \
--SS_lib_type RF \
- --CPU 4
+ --CPU ${CPU}
##### Done Running Trinity #####
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe.noSeqtk.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe.noSeqtk.sh
@@ -9,11 +9,12 @@
exit 1
fi
+CPU=$(nproc || sysctl -n hw.physicalcpu)
${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
--left reads.left.fq.gz \
--right reads.right.fq.gz \
--SS_lib_type RF \
- --CPU 4 \
+ --CPU ${CPU} \
--output trinity_out_dir_noseqtk --NO_SEQTK
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_include_supertranscripts.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_include_supertranscripts.sh
@@ -4,11 +4,13 @@
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
+CPU=$(nproc || sysctl -n hw.physicalcpu)
+
${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G \
--left reads.left.fq.gz \
--right reads.right.fq.gz \
--SS_lib_type RF \
- --CPU 4 --include_supertranscripts --output trinity_incl_supertrans
+ --CPU ${CPU} --include_supertranscripts --output trinity_incl_supertrans
exit 0
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_para_iworm.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_para_iworm.sh
@@ -1,5 +1,7 @@
#!/bin/bash -ve
+CPU=$(nproc || sysctl -n hw.physicalcpu)
+
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
@@ -14,7 +16,7 @@
--left reads.left.fq.gz \
--right reads.right.fq.gz \
--SS_lib_type RF \
- --CPU 4 --NO_PARALLEL_IWORM
+ --CPU ${CPU} --NO_PARALLEL_IWORM
##### Done Running Trinity #####
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_salmon_no_cleanup.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_salmon_no_cleanup.sh
@@ -1,5 +1,7 @@
#!/bin/bash -ve
+CPU=$(nproc || sysctl -n hw.physicalcpu)
+
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
@@ -14,7 +16,7 @@
--left reads.left.fq.gz \
--right reads.right.fq.gz \
--SS_lib_type RF \
- --CPU 4 --no_salmon --no_cleanup --verbose
+ --CPU ${CPU} --no_salmon --no_cleanup --verbose
##### Done Running Trinity #####
--- trinityrnaseq.orig/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_wSuperReads.sh
+++ trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_wSuperReads.sh
@@ -1,5 +1,7 @@
#!/bin/bash -ve
+CPU=$(nproc || sysctl -n hw.physicalcpu)
+
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
@@ -14,7 +16,7 @@
--left reads.left.fq.gz \
--right reads.right.fq.gz \
--SS_lib_type RF \
- --CPU 4 --output trinity_out_dir_SR --NO_PARALLEL_IWORM --SUPER_READS --no_cleanup
+ --CPU ${CPU} --output trinity_out_dir_SR --NO_PARALLEL_IWORM --SUPER_READS --no_cleanup
##### Done Running Trinity #####
--- trinityrnaseq.orig/trinity_ext_sample_data/test_InSilicoReadNormalization/test_PE_normalization.mult_read_sets.sh
+++ trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_PE_normalization.mult_read_sets.sh
@@ -1,10 +1,12 @@
#!/bin/bash -ve
+CPU=$(nproc || sysctl -n hw.physicalcpu)
+
# just for testing purposes, use --max_cov 30 or higher for real applications.
$TRINITY_HOME/util/insilico_read_normalization.pl --JM 2G \
--left ../test_DATA/reads.left.fq.gz,../test_DATA/reads2.left.fq.gz \
--right ../test_DATA/reads.right.fq.gz,../test_DATA/reads2.right.fq.gz \
- --seqType fq --max_cov 5 --pairs_together --no_cleanup --CPU 4 --tmp_dir_name tmp_PE_mult_norm_dir \
+ --seqType fq --max_cov 5 --pairs_together --no_cleanup --CPU ${CPU} --tmp_dir_name tmp_PE_mult_norm_dir \
--output test_multi_read_sets_norm_outdir
--- trinityrnaseq.orig/trinity_ext_sample_data/test_InSilicoReadNormalization/test_PE_normalization.sh
+++ trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_PE_normalization.sh
@@ -1,7 +1,9 @@
#!/bin/bash -ve
+CPU=$(nproc || sysctl -n hw.physicalcpu)
+
# just for testing purposes, use --max_cov 30 or higher for real applications.
-$TRINITY_HOME/util/insilico_read_normalization.pl --JM 2G --left ../test_DATA/reads.left.fq.gz --right ../test_DATA/reads.right.fq.gz --seqType fq --max_cov 5 --pairs_together --no_cleanup --CPU 4 --tmp_dir_name tmp_PE_norm_dir --min_cov 2
+$TRINITY_HOME/util/insilico_read_normalization.pl --JM 2G --left ../test_DATA/reads.left.fq.gz --right ../test_DATA/reads.right.fq.gz --seqType fq --max_cov 5 --pairs_together --no_cleanup --CPU ${CPU} --tmp_dir_name tmp_PE_norm_dir --min_cov 2
--- trinityrnaseq.orig/util/support_scripts/tests/tests.py
+++ trinityrnaseq/util/support_scripts/tests/tests.py
@@ -13,6 +13,7 @@
# Trinity
# Copy the .gz files in sample_data/test_Trinity_Assembly to current directory
# Run using nosetests
+CPUT = len(os.sched_getaffinity(0))
MEM_FLAG = "--max_memory 2G"
TEMP_FILES = ['both.fa', 'inchworm.K25.L25.fa', 'jellyfish.kmers.fa']
@@ -32,7 +33,7 @@
def test_sample_data_seq_count(self):
print "When assembling the sample data, the number of sequences assembled should be between 75 and 100"
self.trinity(
- "Trinity --seqType fq %s --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4 --no_cleanup" % MEM_FLAG)
+ "Trinity --seqType fq %s --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU %d --no_cleanup" % (MEM_FLAG, CPU))
handle = open("trinity_out_dir/Trinity.fasta", "rU")
seq_count = len([x for x in SeqIO.parse(handle, "fasta")])
handle.close()
@@ -41,7 +42,7 @@
def test_sample_data_trimmed_and_normalized(self):
print "When assembling the sample data with the --trimmomatic --normalize_reads flags, the number of sequences assembled should be between 75 and 85"
self.trinity(
- "Trinity --seqType fq %s --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" % MEM_FLAG)
+ "Trinity --seqType fq %s --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU %d --trimmomatic --normalize_reads --no_cleanup" % (MEM_FLAG, CPU))
handle = open("trinity_out_dir/Trinity.fasta", "rU")
seq_count = len([x for x in SeqIO.parse(handle, "fasta")])
handle.close()
@@ -50,14 +51,14 @@
def test_no_cleanup_leaves_temp_files(self):
print "The --no_cleanup flag should ensure that the output directory is left behind"
self.trinity(
- "Trinity --seqType fq %s --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4 --no_cleanup" % MEM_FLAG)
+ "Trinity --seqType fq %s --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU %d --no_cleanup" % (MEM_FLAG, CPU))
for f in TEMP_FILES:
self.assertTrue(os.path.exists("trinity_out_dir/%s" % f), msg="%s not found with no_cleanup" % f)
def test_cleanup_removes_temp_files(self):
print "The --full_cleanup flag should ensure that the output directory is gone but the output file remains"
self.trinity(
- "Trinity --seqType fq %s --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4 --full_cleanup" % MEM_FLAG)
+ "Trinity --seqType fq %s --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU %d --full_cleanup" % (MEM_FLAG, CPU))
time.sleep(5) # Make sure the system has time to recognize the directory is gone
self.assertFalse(os.path.exists("trinity_out_dir"), msg="Did full_cleanup but trinity_out_dir exists")
self.assertTrue(os.path.isfile("trinity_out_dir.Trinity.fasta"),
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