+++ /dev/null
-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
- <maintainer@bioconductor.org>
-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
+++ /dev/null
-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 functions to return package names
- associated with Bioconductor publications.
-biocinstallRepos Display current Bioconductor and CRAN
- repositories.
-useDevel Get the 'devel' version of the BiocInstaller
- package.
+++ /dev/null
-import("utils")
-
-export(biocLite, biocVersion, biocinstallRepos, useDevel, biocValid,
- monograph_group, RBioinf_group, biocases_group, all_group)
+++ /dev/null
-CHANGES IN VERSION 1.10.0
--------------------------
-
-NEW FEATURES
-
- o biocValid() checks that installed packages are consistent with
- those available via biocLite().
-
- o biocVersion() returns the version of Bioconductor expected with
- this version of the BiocInstaller package.
-
-USER-VISIBLE CHANGES
-
- o biocLite() invoked with no arguments updates currently installed
- packages to their most-recent version.
-
+++ /dev/null
-# File share/R/nspackloader.R
-# Part of the R package, http://www.R-project.org
-#
-# Copyright (C) 1995-2012 The R Core Team
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# A copy of the GNU General Public License is available at
-# http://www.r-project.org/Licenses/
-
-local({
- info <- loadingNamespaceInfo()
- pkg <- info$pkgname
- ns <- .getNamespace(as.name(pkg))
- if (is.null(ns))
- stop("cannot find namespace environment for ", pkg, domain = NA);
- dbbase <- file.path(info$libname, pkg, "R", pkg)
- lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
-})
+++ /dev/null
-all_group packageGroups
-biocases_group packageGroups
-biocinstallRepos biocinstallRepos
-biocLite biocLite
-BiocUpgrade BiocUpgrade
-biocValid biocValid
-biocVersion biocVersion
-monograph_group packageGroups
-RBioinf_group packageGroups
-useDevel useDevel
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><title>R: Install/Update Bioconductor and CRAN Packages</title>
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-<link rel="stylesheet" type="text/css" href="R.css">
-</head><body>
-<h1> Install/Update Bioconductor and CRAN Packages
-<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
-</h1>
-<hr>
-<div align="center">
-<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
-<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
-</div><h2>Documentation for package ‘BiocInstaller’ version 1.12.0</h2>
-
-<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
-<li><a href="../NEWS">Package NEWS</a>.</li>
-</ul>
-
-<h2>Help Pages</h2>
-
-
-<table width="100%">
-<tr><td width="25%"><a href="packageGroups.html">all_group</a></td>
-<td>Convenience functions to return package names associated with Bioconductor publications.</td></tr>
-<tr><td width="25%"><a href="packageGroups.html">biocases_group</a></td>
-<td>Convenience functions to return package names associated with Bioconductor publications.</td></tr>
-<tr><td width="25%"><a href="biocinstallRepos.html">biocinstallRepos</a></td>
-<td>Display current Bioconductor and CRAN repositories.</td></tr>
-<tr><td width="25%"><a href="biocLite.html">biocLite</a></td>
-<td>Install or update Bioconductor and CRAN packages</td></tr>
-<tr><td width="25%"><a href="BiocUpgrade.html">BiocUpgrade</a></td>
-<td>Upgrade Bioconductor to the latest version available for this version of R</td></tr>
-<tr><td width="25%"><a href="biocValid.html">biocValid</a></td>
-<td>Validate installed package versions against biocLite versions.</td></tr>
-<tr><td width="25%"><a href="biocVersion.html">biocVersion</a></td>
-<td>Bioconductor version</td></tr>
-<tr><td width="25%"><a href="packageGroups.html">monograph_group</a></td>
-<td>Convenience functions to return package names associated with Bioconductor publications.</td></tr>
-<tr><td width="25%"><a href="packageGroups.html">RBioinf_group</a></td>
-<td>Convenience functions to return package names associated with Bioconductor publications.</td></tr>
-<tr><td width="25%"><a href="useDevel.html">useDevel</a></td>
-<td>Get the 'devel' version of the BiocInstaller package.</td></tr>
-</table>
-</body></html>
+++ /dev/null
-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%);
-}
-
+++ /dev/null
-## 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, ...)
- }
- }
-})
+++ /dev/null
-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)))
- }
-}
+++ /dev/null
-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]])
-}
$(CC) -O3 -Wall calcClusteringInfo.cpp -o $@
clean :
- rm -rf blockmodeling $(PROGRAMS) *~
+ rm -rf blockmodeling $(PROGRAMS) *~ BiocInstaller
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.
## <a name="license"></a> License
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, $out_file) = ();
my @tmp_dirs = ();
pod2usage(-msg => "Input file's suffix is neither sam nor bam!", -exitval => 2, -verbose => 2) if (($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: $temp_dir exists, convert-sam-for-rsem will write temporary files into this folder and delete it after it finishes!\n"; }
else {
if (!$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 {
# 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
# 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__
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;
"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
}
# 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";
}
# 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) { $time_start = time(); }
if ($mTime) { $time_start = time(); }
-$command = $dir."rsem-parse-alignments $refName $imdName $statName";
+$command = "rsem-parse-alignments $refName $imdName $statName";
my $samInpType;
if ($is_sam) { $samInpType = "s"; }
&runCommand($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 $imdName\_alignable_2.fa"; }
print OUTPUT "$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 $fn_list"; }
}
if ($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);
}
}
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) { $command .= " -q"; }
}
if ($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);
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 $help = 0;
pod2usage(-verbose => 2) if ($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__
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 $transcript_list = 0; # default is 0, this option can only be turned on if allele-specific expression is calculated
pod2usage(-msg => "--transcript-list cannot be set if allele-specific reference is not built!", -exitval => 2, -verbose => 2) if (!$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);
}
}
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__
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 $gtfF = "";
if ($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";
}
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 { $command .= " 0"; }
&runCommand($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"; }
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 $help = 0;
pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 3);
pod2usage(-msg => "ngvector file cannot be named as #! # is reserved for other purpose!", -exitval => 2, -verbose => 2) if ($ngvF eq "#");
-my $dir = "$FindBin::Bin/";
my $command = "";
my @conditions = split(/,/, $ARGV[1]);
if ($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__
close(OUTPUT);
}
-# dir
+# 0, dir
sub showVersionInfo {
- open(INPUT, "$_[0]\WHAT_IS_NEW");
+ open(INPUT, "$_[0]/WHAT_IS_NEW");
my $line = <INPUT>;
chomp($line);
close(INPUT);
projects / rsem.git / commitdiff