Mercurial > repos > stef > qdnaseq_test
changeset 9:4efd258b33d9 draft
Uploaded
author | stef |
---|---|
date | Fri, 31 Oct 2014 07:13:53 -0400 |
parents | 238a698f7904 |
children | 0e5432d467fa |
files | QDNAseq.R QDNAseq.xml tool_dependencies.xml |
diffstat | 3 files changed, 20 insertions(+), 22 deletions(-) [+] |
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--- a/QDNAseq.R Mon Oct 27 05:38:16 2014 -0400 +++ b/QDNAseq.R Fri Oct 31 07:13:53 2014 -0400 @@ -135,9 +135,13 @@ ## ================================================== ## Start of analysis ## ================================================== +cmdLineArgs <- commandArgs(TRUE) +config <- cmdLineArgs[1] +installDir <- cmdLineArgs[2] + MAIN_NAME <- '[INFO] ' TOOL_PATH <- getScriptPath() -CSS_FILE <- paste( TOOL_PATH, '/static/css/QDNAseq.css', sep="" ) +CSS_FILE <- paste( installDir, '/static/css/QDNAseq.css', sep="" ) DECIMALS <- 3 WEB_LINK <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html' PURE_CSS <- 'http://yui.yahooapis.com/pure/0.5.0/pure-min.css' @@ -146,20 +150,9 @@ catMsg( "Loading R libraries" ) catMsg( R.version.string ) -packs <- c( "limma", "marray", "CGHbase", "impute", "DNAcopy", "CGHcall" ) -for ( pack in packs ){ - catMsg( c("Loading ", pack) ) - library( pack ) -} - -## supress msg to allow R to finish with non-error msg suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) ) suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) ) -## only one param: the tmp config file -cmdLineArgs <- commandArgs(TRUE) -config <- cmdLineArgs[1] - ## sourcing the config file will load all input params ## many variables are imported via sourced "config" source( config )
--- a/QDNAseq.xml Mon Oct 27 05:38:16 2014 -0400 +++ b/QDNAseq.xml Fri Oct 31 07:13:53 2014 -0400 @@ -3,8 +3,8 @@ <requirements> <!-- R 3.1.0 dependency will be used instead when available, now default R is used, see command --> - <requirement type="package" version="3.1.0">R</requirement> - <requirement type="package" version="1.0.5">qdnaseq</requirement> + <!-- <requirement type="package" version="3.1.0">R</requirement> --> + <!-- <requirement type="package" version="1.0.5">qdnaseq</requirement> --> <requirement type="package" version="0.1.18">samtools</requirement> </requirements> @@ -14,6 +14,7 @@ <command interpreter="Rscript"> QDNAseq.R $qdnaseq_cfg + $INSTALL_DIR </command> <stdio>
--- a/tool_dependencies.xml Mon Oct 27 05:38:16 2014 -0400 +++ b/tool_dependencies.xml Fri Oct 31 07:13:53 2014 -0400 @@ -2,24 +2,28 @@ <tool_dependency> <package name="samtools" version="0.1.18"> - <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="TRUE" /> </package> <!-- As soon as R 3_1_0 package works good, all dependencies will be set via "package_qdnaseq_1_0_5" --> <!-- Currently these have to be manually installed by installing Bioconductor package "QDNAseq" --> + <!-- <package name="R" version="3.1.0"> - <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="TRUE" /> </package> - - <package name="qdnaseq" version="1.0.5"> - <repository changeset_revision="8473e3b3c386" name="package_qdnaseq_1_0_5" owner="stef" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> + --> <!-- + <package name="qdnaseq" version="1.0.5"> + <repository name="package_qdnaseq_1_0_5" owner="stef"/> + </package> + --> + + <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + <environment_variable name="INSTALL_DIR" action="prepend_to">$INSTALL_DIR</environment_variable> </action> - --> + </tool_dependency>