Mercurial > repos > saskia-hiltemann > igv_screenshot
changeset 0:aad38011de33 draft default tip
Uploaded
| author | saskia-hiltemann |
|---|---|
| date | Tue, 28 Jul 2015 11:16:53 -0400 |
| parents | |
| children | |
| files | README igvscreenshot.sh igvscreenshot.xml tool_dependencies.xml |
| diffstat | 4 files changed, 254 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue Jul 28 11:16:53 2015 -0400 @@ -0,0 +1,29 @@ +IGV screenshot tool + +Installation +----------------------- +IMPORTANT: this tool assumes java runtime and Xvfb to be installed on the system! + +installing Xvfb on Ubuntu: + apt-get install Xvfb + + +Dependencies +---------------------- +Dependencies installed with this tool: IGV version 2.3.57 + + +Troubleshooting +----------------------- +tested on Ubuntu, IGV seems quite fussy depending on version.. + +-- +If you get this error: +(process:52487): GLib-GIO-ERROR **: Settings schema 'org.gnome.system.proxy' is not installed + +Fix by installing: +sudo apt-get install gsettings-desktop-schemas +-- + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/igvscreenshot.sh Tue Jul 28 11:16:53 2015 -0400 @@ -0,0 +1,115 @@ +# Get igv screenshot + +echo $@ + +# parse input parameters +set -- `getopt -n$0 -u -a --longoptions="track: region: archive: build: outfile: scriptdir: ftype: index: label: viewaspairs: view:" "h:" "$@"` || usage +[ $# -eq 0 ] && usage + +while [ $# -gt 0 ] +do + case "$1" in + --track) tracks+=",$2";shift;; + --region) region=$2;shift;; + --build) build=$2;shift;; + --outfile) outfile=$2;shift;; + --scriptdir) scriptdir=$2;shift;; + --ftype) ftypes+=",$2";shift;; + --index) indexfiles+=",$2";shift;; + --label) tracklabels+=",$2";shift;; + --view) view+=",$2";shift;; + --viewaspairs) viewaspairs+=",$2";shift;; + -h) shift;; + --) shift;break;; + -*) usage;; + *) break;; + esac + shift +done + +# location of IGV installation +igvlocation="${scriptdir}/IGV_2.1.28" + +# set preferences properly +echo -e "IGV.track.show.attribute.views=true +LAST_CHROMOSOME_VIEWED_KEY=All +DEFAULT_GENOME_KEY=${build}" > prefs.properties + +#IGV.Bounds=0,0,$width,$height +#SHOW_SEQUENCE_TRANSLATION=true +#IGV.Frame.ExtendedState=0 + +# parse track, filetype and indexfile strings +tracks=${tracks/,/} # remove leading comma from list +tracks=${tracks//,/ } # replace commas with spaces +ftypes=${ftypes/,/} # remove leading comma from list +indexfiles=${indexfiles/,/} # remove leading comma from list +tracklabels=${tracklabels/,/} # remove leading comma from list +tracklabels=${tracklabels// /_} # replace spaces with underscores for track labels +view=${view/,/} # remove leading comma from list +viewaspairs=${viewaspairs/,/} # remove leading comma from list + +# generate batch file recipe for igv +echo -e "new +genome ${build}" > recipe.txt + +# add tracks to recipe +IFS=',' read -a ftypearray <<< "$ftypes" +IFS=',' read -a indexarray <<< "$indexfiles" +IFS=',' read -a labelarray <<< "$tracklabels" +IFS=',' read -a viewarray <<< "$view" +IFS=',' read -a viewaspairsarray <<< "$viewaspairs" +count=0 +for track in $tracks +do + + # make symlink to file with the proper extension (or IGV will not work) + ftype=${ftypearray[count]} + label=${labelarray[count]} + ltrack="${label}.${ftype}" + ln -s ${track} ${ltrack} + + # link the index file too if needed + if [[ $ftype == "bam" ]] + then + indexltrack="${label}.bam.bai" + ln -s ${indexarray[count]} ${indexltrack} + fi + + # add track to recipe + echo -e "load ${ltrack}" >>recipe.txt + + # set view for track (collapsed/expanded/squished) + echo -e "${viewarray[count]} ${ltrack}" >> recipe.txt + + # set to view as pairs if requested + if [[ ${viewaspairsarray[count]} == "yes" ]] + then + echo -e "viewaspairs ${ltrack}" >> recipe.txt + fi + + + count=$[$count+1] + +done + + +echo -e "snapshotDirectory . +goto ${region//,/ } +sort base +snapshot screenshot.png +exit" >> recipe.txt + +# for debugging purposes: +echo -e "\nIGV batch recipe is:\n" +cat recipe.txt + +# setup X environment +echo -e "\nsetting up Xvfb:\n" +Xvfb :0 2>&1 & +export DISPLAY=:0 + +# run igv +echo -e "\nrunning IGV:\n" +igv.sh -b recipe.txt -o prefs.properties 2>&1 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/igvscreenshot.xml Tue Jul 28 11:16:53 2015 -0400 @@ -0,0 +1,84 @@ +<tool id="igvscreenshot" name="Take an IGV screenshot" version="1.2"> + + <description>specifying tracks and a genomic location</description> + + <requirements> + <requirement type="package" version="2.3.57">igv</requirement> + </requirements> + + + <command interpreter="bash"> + igvscreenshot.sh + --build $reference + #for $i, $t in enumerate( $tracks ) + --track ${t.inputfile} + --ftype ${t.inputfile.extension} + --view ${t.view} + --viewaspairs ${t.viewaspairs} + #if not $t.trackname <!-- validator for empty field does not seem to work within a repeat, so this is the workaround --> + #set $tracklabel = "noname" + #else + #set $tracklabel = $t.trackname + #end if + --label $tracklabel + #if $t.inputfile.extension == "bam" + --index $t.inputfile.metadata.bam_index + #else + --index "none" + #end if + #end for + --region "$region" + </command> + + + <inputs> + <!-- parameter examples, see https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax for descriptions --> + + <param name="reference" type="select" label="Select Build"> + <option value="hg18"> hg18 </option> + <option value="hg19"> hg19 </option> + </param> + + <!-- file from history --> + <repeat name="tracks" title="Track" min="1"> + <param name="inputfile" type="data" format="bam,vcf,bed,gtf,gff" label="Select input file" help="choose input file from history"/> + <param name="trackname" type="text" size="100" value="track label" label="Track Label" > + <sanitizer> + <valid initial="default"> + <add preset="string.printable"/> + <remove value=" "/> + </valid> + <mapping initial="none"> + <add source=" " target="_"/> + </mapping> + </sanitizer> + </param> + <param name="view" type="select" label="View settings of track" > + <option value="collapse" > collapsed </option> + <option value="expand" > expanded </option> + <option value="squish" > squished </option> + </param> + <param name="viewaspairs" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="view as pairs?" help="optional setting for paired-end data"/> + + </repeat> + <!-- text field parameter --> + <param name="region" type="text" size="100" value="chr:start-end" label="Enter region to visualise in IGV, format chr:start-end" help="to show multiple regions in a single image, use comma-separated list of regions, e.g. chr1:0-100,chr2:100-200"/> + + </inputs> + + + <outputs> + <data format="png" name="outputfile" from_work_dir="screenshot.png" label="IGV screenshot of region ${region} on ${on_string}"/> + </outputs> + + <help> +This tool will create an IGV screenshot of the desired location(s) with the desired tracks. + +Tracks may be bam, vcf, bed, gff or gtf format. + +Multiple regions may be specified (comma-separated) + + + + </help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jul 28 11:16:53 2015 -0400 @@ -0,0 +1,26 @@ +<?xml version="1.0"?> + +<tool_dependency> + <package name="igv" version="2.3.57"> + + <install version="1.0"> + <actions> + <action type="download_by_url"> http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.57.zip</action> + <action type="shell_command"> chmod a+x igv.sh</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + + </install> + + <readme> + Downloads and installs the igv 2.3.57 package. + </readme> + </package> +</tool_dependency> +