From f49d6d79ed79ffed38df6f80dd15b6d09f1ec8ab Mon Sep 17 00:00:00 2001 From: Bo Li Date: Thu, 3 Apr 2014 12:30:24 -0500 Subject: [PATCH] Use PATH env to instead the variable --- EBSeq/BiocInstaller/DESCRIPTION | 13 --- EBSeq/BiocInstaller/INDEX | 13 --- EBSeq/BiocInstaller/Meta/Rd.rds | Bin 567 -> 0 bytes EBSeq/BiocInstaller/Meta/hsearch.rds | Bin 578 -> 0 bytes EBSeq/BiocInstaller/Meta/links.rds | Bin 238 -> 0 bytes EBSeq/BiocInstaller/Meta/nsInfo.rds | Bin 272 -> 0 bytes EBSeq/BiocInstaller/Meta/package.rds | Bin 630 -> 0 bytes EBSeq/BiocInstaller/NAMESPACE | 4 - EBSeq/BiocInstaller/NEWS | 16 ---- EBSeq/BiocInstaller/R/BiocInstaller | 27 ------ EBSeq/BiocInstaller/R/BiocInstaller.rdb | Bin 16249 -> 0 bytes EBSeq/BiocInstaller/R/BiocInstaller.rdx | Bin 958 -> 0 bytes EBSeq/BiocInstaller/help/AnIndex | 10 -- EBSeq/BiocInstaller/help/BiocInstaller.rdb | Bin 21720 -> 0 bytes EBSeq/BiocInstaller/help/BiocInstaller.rdx | Bin 311 -> 0 bytes EBSeq/BiocInstaller/help/aliases.rds | Bin 185 -> 0 bytes EBSeq/BiocInstaller/help/paths.rds | Bin 193 -> 0 bytes EBSeq/BiocInstaller/html/00Index.html | 44 --------- EBSeq/BiocInstaller/html/R.css | 57 ------------ EBSeq/BiocInstaller/scripts/biocLite.R | 86 ------------------ .../unitTests/test_BiocUpgrade.R | 29 ------ .../unitTests/test_biocinstallRepos.R | 27 ------ EBSeq/makefile | 2 +- README.md | 2 +- convert-sam-for-rsem | 18 ++-- rsem-calculate-expression | 38 ++++---- rsem-generate-ngvector | 15 +-- rsem-plot-transcript-wiggles | 22 +++-- rsem-prepare-reference | 16 ++-- rsem-run-ebseq | 13 ++- rsem_perl_utils.pm | 4 +- 31 files changed, 73 insertions(+), 383 deletions(-) delete mode 100644 EBSeq/BiocInstaller/DESCRIPTION delete mode 100644 EBSeq/BiocInstaller/INDEX delete mode 100644 EBSeq/BiocInstaller/Meta/Rd.rds delete mode 100644 EBSeq/BiocInstaller/Meta/hsearch.rds delete mode 100644 EBSeq/BiocInstaller/Meta/links.rds delete mode 100644 EBSeq/BiocInstaller/Meta/nsInfo.rds delete mode 100644 EBSeq/BiocInstaller/Meta/package.rds delete mode 100644 EBSeq/BiocInstaller/NAMESPACE delete mode 100644 EBSeq/BiocInstaller/NEWS delete mode 100644 EBSeq/BiocInstaller/R/BiocInstaller delete mode 100644 EBSeq/BiocInstaller/R/BiocInstaller.rdb delete mode 100644 EBSeq/BiocInstaller/R/BiocInstaller.rdx delete mode 100644 EBSeq/BiocInstaller/help/AnIndex delete mode 100644 EBSeq/BiocInstaller/help/BiocInstaller.rdb delete mode 100644 EBSeq/BiocInstaller/help/BiocInstaller.rdx delete mode 100644 EBSeq/BiocInstaller/help/aliases.rds delete mode 100644 EBSeq/BiocInstaller/help/paths.rds delete mode 100644 EBSeq/BiocInstaller/html/00Index.html delete mode 100644 EBSeq/BiocInstaller/html/R.css delete mode 100644 EBSeq/BiocInstaller/scripts/biocLite.R delete mode 100644 EBSeq/BiocInstaller/unitTests/test_BiocUpgrade.R delete mode 100644 EBSeq/BiocInstaller/unitTests/test_biocinstallRepos.R diff --git a/EBSeq/BiocInstaller/DESCRIPTION b/EBSeq/BiocInstaller/DESCRIPTION deleted file mode 100644 index 269c539..0000000 --- a/EBSeq/BiocInstaller/DESCRIPTION +++ /dev/null @@ -1,13 +0,0 @@ -Package: BiocInstaller -Title: Install/Update Bioconductor and CRAN Packages -Description: Installs/updates Bioconductor and CRAN packages -Version: 1.12.0 -Author: Dan Tenenbaum and Biocore Team -Maintainer: Bioconductor Package Maintainer - -biocViews: Software -Depends: R (>= 3.0.0) -Suggests: RUnit, BiocGenerics -License: Artistic-2.0 -Packaged: 2013-10-15 04:03:53 UTC; biocbuild -Built: R 3.0.2; ; 2013-10-15 11:47:50 UTC; unix diff --git a/EBSeq/BiocInstaller/INDEX b/EBSeq/BiocInstaller/INDEX deleted file mode 100644 index ec33cf3..0000000 --- a/EBSeq/BiocInstaller/INDEX +++ /dev/null @@ -1,13 +0,0 @@ -BiocUpgrade Upgrade Bioconductor to the latest version - available for this version of R -biocLite Install or update Bioconductor and CRAN - packages -biocValid Validate installed package versions against - biocLite versions. -biocVersion Bioconductor version -biocases_group Convenience 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n`_;(AGy3Ono5mU|P3}J1niVomncECb;=$_;HL^#nya50J2W3@~ diff --git a/EBSeq/BiocInstaller/help/paths.rds b/EBSeq/BiocInstaller/help/paths.rds deleted file mode 100644 index 7b4a225d01866aa83b96aa3120f2dfd94b8bb3bf..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 193 zcmV;y06za8iwFP!000001Fg}|3xY5d2k@am)TzJ32|{`;q>zThtmwMjOGeX;O@;pZ zh6Q%l!~4Pa@PWs>uMt8X@?CkpThYeV5-rfm%^YhZde#DNYmKRE??alJ2-6_Ti_4A> zz74}DPQqsyCwMPZnKia$Qi8!XYlh^iE5kShl>gMzRQ2H!BHBNa%t79m6nr!%A3vC2 vtWeFU7IUcLn^4foj`Vpdty%eE6&#J~w4L!^orM&7kdFKSCY5Y%Zvp@SATeEF diff --git a/EBSeq/BiocInstaller/html/00Index.html b/EBSeq/BiocInstaller/html/00Index.html deleted file mode 100644 index 33a3a2e..0000000 --- a/EBSeq/BiocInstaller/html/00Index.html +++ /dev/null @@ -1,44 +0,0 @@ - -R: Install/Update Bioconductor and CRAN Packages - - - -

Install/Update Bioconductor and CRAN Packages - -

-
-
-[Up] -[Top] -

Documentation for package ‘BiocInstaller’ version 1.12.0

- - - -

Help Pages

- - - - - - - - - - - - - - - - - - - - - - - -
all_groupConvenience functions to return package names associated with Bioconductor publications.
biocases_groupConvenience functions to return package names associated with Bioconductor publications.
biocinstallReposDisplay current Bioconductor and CRAN repositories.
biocLiteInstall or update Bioconductor and CRAN packages
BiocUpgradeUpgrade Bioconductor to the latest version available for this version of R
biocValidValidate installed package versions against biocLite versions.
biocVersionBioconductor version
monograph_groupConvenience functions to return package names associated with Bioconductor publications.
RBioinf_groupConvenience functions to return package names associated with Bioconductor publications.
useDevelGet the 'devel' version of the BiocInstaller package.
- diff --git a/EBSeq/BiocInstaller/html/R.css b/EBSeq/BiocInstaller/html/R.css deleted file mode 100644 index 6f058f3..0000000 --- a/EBSeq/BiocInstaller/html/R.css +++ /dev/null @@ -1,57 +0,0 @@ -BODY{ background: white; - color: black } - -A:link{ background: white; - color: blue } -A:visited{ background: white; - color: rgb(50%, 0%, 50%) } - -H1{ background: white; - color: rgb(55%, 55%, 55%); - font-family: monospace; - font-size: x-large; - text-align: center } - -H2{ background: white; - color: rgb(40%, 40%, 40%); - font-family: monospace; - font-size: large; - text-align: center } - -H3{ background: white; - color: rgb(40%, 40%, 40%); - font-family: monospace; - font-size: large } - -H4{ background: white; - color: rgb(40%, 40%, 40%); - font-family: monospace; - font-style: italic; - font-size: large } - -H5{ background: white; - color: rgb(40%, 40%, 40%); - font-family: monospace } - -H6{ background: white; - color: rgb(40%, 40%, 40%); - font-family: monospace; - font-style: italic } - -IMG.toplogo{ vertical-align: middle } - -IMG.arrow{ width: 30px; - height: 30px; - border: 0 } - -span.acronym{font-size: small} -span.env{font-family: monospace} -span.file{font-family: monospace} -span.option{font-family: monospace} -span.pkg{font-weight: bold} -span.samp{font-family: monospace} - -div.vignettes a:hover { - background: rgb(85%, 85%, 85%); -} - diff --git a/EBSeq/BiocInstaller/scripts/biocLite.R b/EBSeq/BiocInstaller/scripts/biocLite.R deleted file mode 100644 index 9940cfb..0000000 --- a/EBSeq/BiocInstaller/scripts/biocLite.R +++ /dev/null @@ -1,86 +0,0 @@ -## Mirrors: uncomment the following and change to your favorite CRAN mirror -## if you don't want to use the default (cran.fhcrc.org, Seattle, USA). -## options("repos" = c(CRAN="http://cran.fhcrc.org")) - -## Mirrors: uncomment the following and change to your favorite Bioconductor -## mirror, if you don't want to use the default (www.bioconductor.org, -## Seattle, USA) -## options("BioC_mirror" = "http://www.bioconductor.org") - -local({ - currBiocVers <- - package_version(readLines("http://bioconductor.org/bioc-version", - warn=FALSE)) - vers <- getRversion() - biocVers <- tryCatch({ - BiocInstaller::biocVersion() # recent BiocInstaller - }, error=function(...) { # no / older BiocInstaller - tools:::.BioC_version_associated_with_R_version - }) - - if (biocVers < currBiocVers) { - txt <- strwrap(sprintf("Your Bioconductor is out-of-date, upgrade - to version %s by following instructions at - http://bioconductor.org/install.", currBiocVers)) - message(paste(txt, collapse="\n")) - } - - if (vers > "2.13" && biocVers > "2.8") { - - if (exists("biocLite", .GlobalEnv, inherits=FALSE)) { - txt <- strwrap("There is an outdated biocLite() function in the - global environment; run 'rm(biocLite)' and try again.") - stop("\n", paste(txt, collapse="\n")) - } - - if (!suppressWarnings(require("BiocInstaller", quietly=TRUE))) { - a <- NULL - p <- file.path(Sys.getenv("HOME"), ".R", "repositories") - if (file.exists(p)) { - a <- tools:::.read_repositories(p) - if (!"BioCsoft" %in% rownames(a)) - a <- NULL - } - if (is.null(a)) { - p <- file.path(R.home("etc"), "repositories") - a <- tools:::.read_repositories(p) - } - if (!"package:utils" %in% search()) { - url <- "http://bioconductor.org/biocLite.R" - txt <- sprintf("use 'source(\"%s\")' to update 'BiocInstaller' - after 'utils' package is attached", - url) - message(paste(strwrap(txt), collapse="\n ")) - } else { - ## add a conditional for Bioc releases occuring WITHIN - ## a single R minor version - if (vers >= "2.15" && vers < "2.16") { - a["BioCsoft", "URL"] <- sub(as.character(biocVers), "2.11", - a["BioCsoft", "URL"]) - biocVers <- numeric_version("2.11") - } - install.packages("BiocInstaller", repos=a["BioCsoft", "URL"]) - if (!suppressWarnings(require("BiocInstaller", - quietly=TRUE))) { - url0 <- "http://www.bioconductor.org/packages" - url <- sprintf("%s/%s/bioc", - url0, as.character(biocVers)) - txt0 <- "'biocLite.R' failed to install 'BiocInstaller', - use 'install.packages(\"%s\", repos=\"%s\")'" - txt <- sprintf(txt0, "BiocInstaller", url) - message(paste(strwrap(txt), collapse="\n ")) - } - } - } - } else { - source("http://bioconductor.org/getBioC.R") - biocLite <<- - function(pkgs, groupName="lite", ...) - { - if (missing(pkgs)) - biocinstall(groupName=groupName, ...) - else - biocinstall(pkgs=pkgs, groupName=groupName, ...) - } - } -}) diff --git a/EBSeq/BiocInstaller/unitTests/test_BiocUpgrade.R b/EBSeq/BiocInstaller/unitTests/test_BiocUpgrade.R deleted file mode 100644 index d4cb4e7..0000000 --- a/EBSeq/BiocInstaller/unitTests/test_BiocUpgrade.R +++ /dev/null @@ -1,29 +0,0 @@ -test_useDevel <- function() -{ - if (!BiocInstaller:::IS_END_OF_LIFE) { - checkException(useDevel(), silent=TRUE) - } else if (!BiocInstaller:::IS_DOWNGRADEABLE) { - checkException(useDevel(FALSE), silent=TRUE) - } - if (!BiocInstaller:::IS_UPGRADEABLE) { - checkException(useDevel(), silent=TRUE) - opts <- options(warn=2); on.exit(options(opts)) - checkException(biocLite("BiocUpgrade")) - } -} - -test_getContribUrl_exist <- function() -{ - fun <- BiocInstaller:::.getContribUrl - - vers <- BiocInstaller:::BIOC_VERSION - checkTrue(grepl(vers, fun(vers))) - if (BiocInstaller:::IS_UPGRADEABLE) { - vers <- BiocInstaller:::UPGRADE_VERSION - checkTrue(grepl(vers, fun(vers))) - } - if (BiocInstaller:::IS_DOWNGRADEABLE) { - vers <- BiocInstaller:::DOWNGRADE_VERSION - checkTrue(grepl(vers, fun(vers))) - } -} diff --git a/EBSeq/BiocInstaller/unitTests/test_biocinstallRepos.R b/EBSeq/BiocInstaller/unitTests/test_biocinstallRepos.R deleted file mode 100644 index e6fb520..0000000 --- a/EBSeq/BiocInstaller/unitTests/test_biocinstallRepos.R +++ /dev/null @@ -1,27 +0,0 @@ -repos <- biocinstallRepos() - -test_biocinstallRepos_named_repositories <- function() -{ - - allOS <- c("BioCsoft", "CRAN", "BioCann", "BioCexp", "BioCextra") - windowsOnly <- "CRANextra" - - checkTrue(all(allOS %in% names(repos))) - if (.Platform$OS.type == "windows") - { - checkTrue(windowsOnly %in% names(repos)) - } else { - checkTrue(!windowsOnly %in% names(repos)) - } - -} - -test_biocinstallRepos_noNA_repositories <- function() -{ - checkTrue(!any(is.na(repos))) -} - -test_biocinstallRepos_order <- function() -{ - checkIdentical("BioCsoft", names(repos)[[1]]) -} diff --git a/EBSeq/makefile b/EBSeq/makefile index bf25454..898c8fa 100644 --- a/EBSeq/makefile +++ b/EBSeq/makefile @@ -10,4 +10,4 @@ rsem-for-ebseq-calculate-clustering-info : calcClusteringInfo.cpp $(CC) -O3 -Wall calcClusteringInfo.cpp -o $@ clean : - rm -rf blockmodeling $(PROGRAMS) *~ + rm -rf blockmodeling $(PROGRAMS) *~ BiocInstaller diff --git a/README.md b/README.md index dddf4bd..902e806 100644 --- a/README.md +++ b/README.md @@ -459,7 +459,7 @@ differential expression analysis. We thank earonesty and Dr. Samuel Arvidsson for contributing patches. -We thank Han Lin, j.miller, Joël Fillon and Dr. Samuel G. Younkin for suggesting possible fixes. +We thank Han Lin, j.miller, Joël Fillon, Dr. Samuel G. Younkin and Malcolm Cook for suggesting possible fixes. ## License diff --git a/convert-sam-for-rsem b/convert-sam-for-rsem index c077616..a7300f2 100755 --- a/convert-sam-for-rsem +++ b/convert-sam-for-rsem @@ -2,14 +2,18 @@ use Getopt::Long; use Pod::Usage; -use FindBin; -use lib $FindBin::Bin; use File::Basename; use File::Path 'rmtree'; -use strict; +use FindBin; +use lib $FindBin::RealBin; use rsem_perl_utils; +use Env qw(@PATH); +push(@PATH, $FindBin::RealBin, "$FindBin::RealBin/sam"); + +use strict; + my ($in_file, $out_file) = (); my @tmp_dirs = (); @@ -33,8 +37,6 @@ $suf = lc(substr($suf, 1)); pod2usage(-msg => "Input file's suffix is neither sam nor bam!", -exitval => 2, -verbose => 2) if (($suf ne "sam") && ($suf ne "bam")); my $isSam = ($suf eq "sam"); -$dir = "$FindBin::Bin/"; - my $temp_dir = "$out_file.temp"; if (-d $temp_dir) { print "Warning: $temp_dir exists, convert-sam-for-rsem will write temporary files into this folder and delete it after it finishes!\n"; } else { @@ -47,7 +49,7 @@ my $sam_file; if (!$isSam) { $sam_file = "$temp_dir/input.sam"; - $command = $dir."sam/samtools view -h -o $sam_file $in_file"; + $command = "samtools view -h -o $sam_file $in_file"; &runCommand($command); } else { @@ -70,7 +72,7 @@ $command .= " >> $tmp_sam"; # Phase II, parse the temporary SAM file to make paired-end alignments' two mates adjacent to each other -$command = $dir."rsem-scan-for-paired-end-reads $tmp_sam $out_file"; +$command = "rsem-scan-for-paired-end-reads $tmp_sam $out_file"; &runCommand($command); # delete temporary directory @@ -80,7 +82,7 @@ print STDERR "Conversion is completed. $out_file will be checked by 'rsem-sam-va # Phase III, validate if the resulting bam file is correct -$command = $dir."rsem-sam-validator $out_file"; +$command = "rsem-sam-validator $out_file"; &runCommand($command); __END__ diff --git a/rsem-calculate-expression b/rsem-calculate-expression index a9f26c9..9040272 100755 --- a/rsem-calculate-expression +++ b/rsem-calculate-expression @@ -2,12 +2,16 @@ use Getopt::Long; use Pod::Usage; -use FindBin; -use lib $FindBin::Bin; -use strict; +use FindBin; +use lib $FindBin::RealBin; use rsem_perl_utils qw(runCommand collectResults showVersionInfo); +use Env qw(@PATH); +push(@PATH, $FindBin::RealBin, "$FindBin::RealBin/sam"); + +use strict; + #const my $BURNIN = 200; my $NCV = 1000; @@ -127,10 +131,8 @@ GetOptions("keep-intermediate-files" => \$keep_intermediate_files, "q|quiet" => \$quiet, "h|help" => \$help) or pod2usage(-exitval => 2, -verbose => 2); -my $dir = "$FindBin::Bin/"; - pod2usage(-verbose => 2) if ($help == 1); -&showVersionInfo($dir) if ($version == 1); +&showVersionInfo($FindBin::RealBin) if ($version == 1); #check parameters and options @@ -251,7 +253,7 @@ if (!$is_sam && !$is_bam) { } # pipe to samtools to generate a BAM file - $command .= " | $dir\sam/samtools view -S -b -o $imdName.bam -"; + $command .= " | samtools view -S -b -o $imdName.bam -"; } else { $command = $bowtie2_path."bowtie2"; @@ -286,7 +288,7 @@ if (!$is_sam && !$is_bam) { } # pipe to samtools to generate a BAM file - $command .= " | $dir\sam/samtools view -S -b -o $imdName.bam -"; + $command .= " | samtools view -S -b -o $imdName.bam -"; } if ($mTime) { $time_start = time(); } @@ -301,7 +303,7 @@ if (!$is_sam && !$is_bam) { if ($mTime) { $time_start = time(); } -$command = $dir."rsem-parse-alignments $refName $imdName $statName"; +$command = "rsem-parse-alignments $refName $imdName $statName"; my $samInpType; if ($is_sam) { $samInpType = "s"; } @@ -314,7 +316,7 @@ if ($quiet) { $command .= " -q"; } &runCommand($command); -$command = $dir."rsem-build-read-index $gap"; +$command = "rsem-build-read-index $gap"; if ($read_type == 0) { $command .= " 0 $quiet $imdName\_alignable.fa"; } elsif ($read_type == 1) { $command .= " 1 $quiet $imdName\_alignable.fq"; } elsif ($read_type == 2) { $command .= " 0 $quiet $imdName\_alignable_1.fa $imdName\_alignable_2.fa"; } @@ -333,7 +335,7 @@ print OUTPUT "$mean $sd\n"; print OUTPUT "$L\n"; close(OUTPUT); -$command = $dir."rsem-run-em $refName $read_type $sampleName $imdName $statName -p $nThreads"; +$command = "rsem-run-em $refName $read_type $sampleName $imdName $statName -p $nThreads"; if ($genBamF) { $command .= " -b $samInpType $inpF"; if ($fn_list ne "") { $command .= " 1 $fn_list"; } @@ -356,17 +358,17 @@ else { } if ($genBamF) { - $command = $dir."sam/samtools sort -@ $nThreads -m $SortMem $sampleName.transcript.bam $sampleName.transcript.sorted"; + $command = "samtools sort -@ $nThreads -m $SortMem $sampleName.transcript.bam $sampleName.transcript.sorted"; &runCommand($command); - $command = $dir."sam/samtools index $sampleName.transcript.sorted.bam"; + $command = "samtools index $sampleName.transcript.sorted.bam"; &runCommand($command); if ($genGenomeBamF) { - $command = $dir."rsem-tbam2gbam $refName $sampleName.transcript.bam $sampleName.genome.bam"; + $command = "rsem-tbam2gbam $refName $sampleName.transcript.bam $sampleName.genome.bam"; &runCommand($command); - $command = $dir."sam/samtools sort -@ $nThreads -m $SortMem $sampleName.genome.bam $sampleName.genome.sorted"; + $command = "samtools sort -@ $nThreads -m $SortMem $sampleName.genome.bam $sampleName.genome.sorted"; &runCommand($command); - $command = $dir."sam/samtools index $sampleName.genome.sorted.bam"; + $command = "samtools index $sampleName.genome.sorted.bam"; &runCommand($command); } } @@ -376,7 +378,7 @@ if ($mTime) { $time_end = time(); $time_rsem = $time_end - $time_start; } if ($mTime) { $time_start = time(); } if ($calcPME || $var_opt || $calcCI ) { - $command = $dir."rsem-run-gibbs $refName $imdName $statName $BURNIN $NCV $SAMPLEGAP"; + $command = "rsem-run-gibbs $refName $imdName $statName $BURNIN $NCV $SAMPLEGAP"; $command .= " -p $nThreads"; if ($var_opt) { $command .= " --var"; } if ($quiet) { $command .= " -q"; } @@ -401,7 +403,7 @@ if ($calcPME || $calcCI) { } if ($calcCI) { - $command = $dir."rsem-calculate-credibility-intervals $refName $imdName $statName $CONFIDENCE $NCV $NSPC $NMB"; + $command = "rsem-calculate-credibility-intervals $refName $imdName $statName $CONFIDENCE $NCV $NSPC $NMB"; $command .= " -p $nThreads"; if ($quiet) { $command .= " -q"; } &runCommand($command); diff --git a/rsem-generate-ngvector b/rsem-generate-ngvector index dc874a9..44066b7 100755 --- a/rsem-generate-ngvector +++ b/rsem-generate-ngvector @@ -2,12 +2,16 @@ use Getopt::Long; use Pod::Usage; -use FindBin; -use lib $FindBin::Bin; -use strict; +use FindBin; +use lib $FindBin::RealBin; use rsem_perl_utils; +use Env qw(@PATH); +push(@PATH, "$FindBin::RealBin/EBSeq"); + +use strict; + my $k = 25; my $help = 0; @@ -17,13 +21,12 @@ GetOptions("k=i" => \$k, pod2usage(-verbose => 2) if ($help == 1); pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 2); -my $dir = "$FindBin::Bin/"; my $command = ""; -$command = $dir."EBSeq/rsem-for-ebseq-calculate-clustering-info $k $ARGV[0] $ARGV[1].ump"; +$command = "rsem-for-ebseq-calculate-clustering-info $k $ARGV[0] $ARGV[1].ump"; &runCommand($command); -$command = $dir."EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info $ARGV[1].ump $ARGV[1].ngvec"; +$command = "rsem-for-ebseq-generate-ngvector-from-clustering-info $ARGV[1].ump $ARGV[1].ngvec"; &runCommand($command); __END__ diff --git a/rsem-plot-transcript-wiggles b/rsem-plot-transcript-wiggles index 3aa7e35..1d14a22 100755 --- a/rsem-plot-transcript-wiggles +++ b/rsem-plot-transcript-wiggles @@ -2,11 +2,16 @@ use Getopt::Long; use Pod::Usage; + use FindBin; -use lib $FindBin::Bin; +use lib $FindBin::RealBin; +use rsem_perl_utils; + +use Env qw(@PATH); +push(@PATH, $FindBin::RealBin, "$FindBin::RealBin/sam"); + use strict; -use rsem_perl_utils; my $gene_list = 0; # default is 0, means input is not a gene list my $transcript_list = 0; # default is 0, this option can only be turned on if allele-specific expression is calculated @@ -27,29 +32,28 @@ if (-e "$ARGV[0].alleles.results") { $alleleS = 1; } pod2usage(-msg => "--transcript-list cannot be set if allele-specific reference is not built!", -exitval => 2, -verbose => 2) if (!$alleleS && $transcript_list); pod2usage(-msg => "--gene-list and --transcript-list cannot be set at the same time!", -exitval => 2, -verbose => 2) if ($gene_list && $transcript_list); -my $dir = "$FindBin::Bin/"; my $command = ""; unless (-e "$ARGV[0].transcript.sorted.bam") { - $command = $dir."sam/samtools sort $ARGV[0].transcript.bam $ARGV[0].transcript.sorted"; + $command = "samtools sort $ARGV[0].transcript.bam $ARGV[0].transcript.sorted"; &runCommand($command); } unless (-e "$ARGV[0].transcript.readdepth") { - $command = $dir."rsem-bam2readdepth $ARGV[0].transcript.sorted.bam $ARGV[0].transcript.readdepth"; + $command = "rsem-bam2readdepth $ARGV[0].transcript.sorted.bam $ARGV[0].transcript.readdepth"; &runCommand($command); } if ($show_unique) { unless (-e "$ARGV[0].uniq.transcript.bam") { - $command = $dir."rsem-get-unique $ARGV[0].transcript.bam $ARGV[0].uniq.transcript.bam"; + $command = "rsem-get-unique $ARGV[0].transcript.bam $ARGV[0].uniq.transcript.bam"; &runCommand($command); } unless (-e "$ARGV[0].uniq.transcript.sorted.bam") { - $command = $dir."sam/samtools sort $ARGV[0].uniq.transcript.bam $ARGV[0].uniq.transcript.sorted"; + $command = "samtools sort $ARGV[0].uniq.transcript.bam $ARGV[0].uniq.transcript.sorted"; &runCommand($command); } unless (-e "$ARGV[0].uniq.transcript.readdepth") { - $command = $dir."rsem-bam2readdepth $ARGV[0].uniq.transcript.sorted.bam $ARGV[0].uniq.transcript.readdepth"; + $command = "rsem-bam2readdepth $ARGV[0].uniq.transcript.sorted.bam $ARGV[0].uniq.transcript.readdepth"; &runCommand($command); } } @@ -66,7 +70,7 @@ else { if ($gene_list) { $id_type = 2; } } -$command = $dir."rsem-gen-transcript-plots $ARGV[0] $ARGV[1] $alleleS $id_type $show_unique $ARGV[2]"; +$command = "rsem-gen-transcript-plots $ARGV[0] $ARGV[1] $alleleS $id_type $show_unique $ARGV[2]"; &runCommand($command); __END__ diff --git a/rsem-prepare-reference b/rsem-prepare-reference index 8050356..a74d97d 100755 --- a/rsem-prepare-reference +++ b/rsem-prepare-reference @@ -3,11 +3,14 @@ use Getopt::Long; use Pod::Usage; use FindBin; -use lib $FindBin::Bin; -use strict; - +use lib $FindBin::RealBin; use rsem_perl_utils; +use Env qw(@PATH); +push(@PATH, $FindBin::RealBin); + +use strict; + my $status; my $gtfF = ""; @@ -75,12 +78,11 @@ elsif ($subsetFile ne "") { $polyAChoice = 2; } if ($bowtie_path ne "") { $bowtie_path .= "/"; } if ($bowtie2_path ne "") { $bowtie2_path .= "/"; } -my $dir = "$FindBin::Bin/"; my $command = ""; if ($type == 0) { $"=" "; - $command = $dir."rsem-extract-reference-transcripts $ARGV[1] $quiet $gtfF"; + $command = "rsem-extract-reference-transcripts $ARGV[1] $quiet $gtfF"; if ($mappingF ne "") { $command .= " 1 $mappingF"; } else { $command .= " 0"; } $command .= " @list"; @@ -88,7 +90,7 @@ if ($type == 0) { } else { $"=" "; - $command = $dir."rsem-synthesis-reference-transcripts $ARGV[1] $quiet"; + $command = "rsem-synthesis-reference-transcripts $ARGV[1] $quiet"; if ($mappingF ne "") { $command .= " 1 $mappingF"; } elsif ($alleleMappingF ne "") { $command .= " 2 $alleleMappingF"; } else { $command .= " 0"; } @@ -96,7 +98,7 @@ else { &runCommand($command); } -$command = $dir."rsem-preref $ARGV[1].transcripts.fa $polyAChoice $ARGV[1] -l $polyALen"; +$command = "rsem-preref $ARGV[1].transcripts.fa $polyAChoice $ARGV[1] -l $polyALen"; if ($polyAChoice == 2) { $command .= " -f $subsetFile"; } if ($no_ntog) { $command .= " --no-ntog"; } if ($quiet) { $command .= " -q"; } diff --git a/rsem-run-ebseq b/rsem-run-ebseq index 9693eee..59d35c8 100755 --- a/rsem-run-ebseq +++ b/rsem-run-ebseq @@ -2,12 +2,16 @@ use Getopt::Long; use Pod::Usage; -use FindBin; -use lib $FindBin::Bin; -use strict; +use FindBin; +use lib $FindBin::RealBin; use rsem_perl_utils; +use Env qw(@PATH); +push(@PATH, "$FindBin::RealBin/EBSeq"); + +use strict; + my $ngvF = ""; my $help = 0; @@ -18,7 +22,6 @@ pod2usage(-verbose => 2) if ($help == 1); pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 3); pod2usage(-msg => "ngvector file cannot be named as #! # is reserved for other purpose!", -exitval => 2, -verbose => 2) if ($ngvF eq "#"); -my $dir = "$FindBin::Bin/"; my $command = ""; my @conditions = split(/,/, $ARGV[1]); @@ -28,7 +31,7 @@ pod2usage(-msg => "At least 2 conditions are required for differential expressio if ($ngvF eq "") { $ngvF = "#"; } $" = " "; -$command = $dir."EBSeq/rsem-for-ebseq-find-DE ".$dir."EBSeq $ngvF $ARGV[0] $ARGV[2] @conditions"; +$command = "rsem-for-ebseq-find-DE $FindBin::RealBin/EBSeq $ngvF $ARGV[0] $ARGV[2] @conditions"; &runCommand($command) __END__ diff --git a/rsem_perl_utils.pm b/rsem_perl_utils.pm index 6355f67..078d119 100644 --- a/rsem_perl_utils.pm +++ b/rsem_perl_utils.pm @@ -86,9 +86,9 @@ sub collectResults { close(OUTPUT); } -# dir +# 0, dir sub showVersionInfo { - open(INPUT, "$_[0]\WHAT_IS_NEW"); + open(INPUT, "$_[0]/WHAT_IS_NEW"); my $line = ; chomp($line); close(INPUT); -- 2.39.2