Etchevers:Notebook/STRA6 in eye development/2009/07/06

Genetics of human eye development

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Realization and installing Ubuntu in Paris The reason the RAX and PAX6 files did not upload well to UCSC had more to do with a corruption in the files introduced when Matthias was erasing columns or saving, than with UCSC. But now I have an account on their wiki. Anthony Fejes tells me I should really install FindPeaks 4.0 for proper support. Wow - and check this thread on a chIP-Seq competition out! Results here. Meanwhile at Necker, got the driver for Ubuntu for the Intel 82567LM-3 Gigabit network adapter and did the following: embryo@ubuntu:~$ gunzip e1000e-0.5.18.3.tar.gz embryo@ubuntu:~$ tar -xvf e1000e-0.5.18.3.tar e1000e-0.5.18.3/ e1000e-0.5.18.3/SUMS e1000e-0.5.18.3/src/ e1000e-0.5.18.3/src/e1000_manage.h e1000e-0.5.18.3/src/e1000_defines.h e1000e-0.5.18.3/src/kcompat.h e1000e-0.5.18.3/src/e1000_ich8lan.h e1000e-0.5.18.3/src/Makefile e1000e-0.5.18.3/src/e1000_80003es2lan.c e1000e-0.5.18.3/src/e1000_phy.h e1000e-0.5.18.3/src/e1000_phy.c e1000e-0.5.18.3/src/e1000_regs.h e1000e-0.5.18.3/src/param.c e1000e-0.5.18.3/src/e1000_82571.c e1000e-0.5.18.3/src/netdev.c e1000e-0.5.18.3/src/e1000_mac.h e1000e-0.5.18.3/src/hw.h e1000e-0.5.18.3/src/e1000_mac.c e1000e-0.5.18.3/src/e1000_nvm.c e1000e-0.5.18.3/src/e1000_80003es2lan.h e1000e-0.5.18.3/src/e1000_nvm.h e1000e-0.5.18.3/src/e1000_82571.h e1000e-0.5.18.3/src/kcompat.c e1000e-0.5.18.3/src/e1000_manage.c e1000e-0.5.18.3/src/e1000_ich8lan.c e1000e-0.5.18.3/src/e1000.h e1000e-0.5.18.3/src/ethtool.c e1000e-0.5.18.3/src/kcompat_ethtool.c e1000e-0.5.18.3/e1000e.spec e1000e-0.5.18.3/COPYING e1000e-0.5.18.3/README e1000e-0.5.18.3/pci.updates e1000e-0.5.18.3/e1000e.7 embryo@ubuntu:~$ cd e1000e-0.5.18.3/src embryo@ubuntu:~/e1000e-0.5.18.3/src$ sudo make install make -C /lib/modules/2.6.28-11-generic/build SUBDIRS=/home/embryo/e1000e-0.5.18.3/src modules make[1]: entrant dans le répertoire « /usr/src/linux-headers-2.6.28-11-generic » CC [M] /home/embryo/e1000e-0.5.18.3/src/netdev.o CC [M] /home/embryo/e1000e-0.5.18.3/src/ethtool.o CC [M] /home/embryo/e1000e-0.5.18.3/src/param.o CC [M] /home/embryo/e1000e-0.5.18.3/src/e1000_82571.o CC [M] /home/embryo/e1000e-0.5.18.3/src/e1000_ich8lan.o CC [M] /home/embryo/e1000e-0.5.18.3/src/e1000_80003es2lan.o CC [M] /home/embryo/e1000e-0.5.18.3/src/e1000_mac.o CC [M] /home/embryo/e1000e-0.5.18.3/src/e1000_nvm.o CC [M] /home/embryo/e1000e-0.5.18.3/src/e1000_phy.o CC [M] /home/embryo/e1000e-0.5.18.3/src/e1000_manage.o CC [M] /home/embryo/e1000e-0.5.18.3/src/kcompat.o LD [M] /home/embryo/e1000e-0.5.18.3/src/e1000e.o Building modules, stage 2. MODPOST 1 modules CC /home/embryo/e1000e-0.5.18.3/src/e1000e.mod.o LD [M] /home/embryo/e1000e-0.5.18.3/src/e1000e.ko make[1]: quittant le répertoire « /usr/src/linux-headers-2.6.28-11-generic » gzip -c ../e1000e.7 > e1000e.7.gz # remove all old versions of the driver find /lib/modules/2.6.28-11-generic -name e1000e.ko -exec rm -f {} \; || true find /lib/modules/2.6.28-11-generic -name e1000e.ko.gz -exec rm -f {} \; || true install -D -m 644 e1000e.ko /lib/modules/2.6.28-11-generic/kernel/drivers/net/e1000e/e1000e.ko /sbin/depmod -a || true install -D -m 644 e1000e.7.gz /usr/share/man/man7/e1000e.7.gz man -c -P'cat > /dev/null' e1000e || true man: impossible d'écrire vers /var/cache/man/cat7/e1000e.7.gz en mode catman e1000e. embryo@ubuntu:~/e1000e-0.5.18.3/src$ sudo rmmod e1000e; embryo@ubuntu:~/e1000e-0.5.18.3/src$ sudo insmod /lib/modules/2.6.28-11-generic/kernel/drivers/net/e1000e/e1000e.ko; embryo@ubuntu:~/e1000e-0.5.18.3/src$ sudo modprobe e1000e; Hope that is not all mushed together. Adding a couple spaces in front of each line helps but is not good for the fingers. Heather 13:53, 6 July 2009 (EDT): Needed to perform apt-get update or something along those lines and download some extra 100Mb+ of files. Build according to instructions on Building FindPeaks 4.0 starting with the large ant installation. Next thing to do is get subversion, before trying a command starting with "svn"! embryo@ubuntu:~$ sudo apt-get install subversion then embryo@ubuntu:~$ svn co http://vancouvershortr.svn.sourceforge.net/svnroot/vancouvershortr/trunk There are a lot of files now in the package (171): trunk/jars trunk/.classpath trunk/.project Heather 14:42, 6 July 2009 (EDT): trunk/Changelog.txt trunk/lib trunk/lib/constants.conf trunk/lib/mysql-connector-java-5.1.6-bin.jar trunk/lib/ensj-39.2.jar trunk/lib/junit.jar trunk/src trunk/src/lib trunk/src/lib/IterableIterator.java trunk/src/lib/mysql_wrapper.java trunk/src/lib/SNPDB.java trunk/src/lib/RandomAlignedReadGenerator.java trunk/src/lib/objects trunk/src/lib/objects/AlignedRead.java trunk/src/lib/objects/SNP.java trunk/src/lib/objects/SliderSNP.java trunk/src/lib/objects/SeqReducedAlignedRead.java trunk/src/lib/objects/Aberation.java trunk/src/lib/objects/FFInt.java trunk/src/lib/objects/IntPair.java trunk/src/lib/objects/MAQRyanMap.java trunk/src/lib/objects/SNPLine.java trunk/src/lib/objects/SimpleAlignedRead.java trunk/src/lib/objects/MAQinner.java trunk/src/lib/objects/CounterArray.java trunk/src/lib/objects/Counter.java trunk/src/lib/objects/MinimalLocation.java trunk/src/lib/objects/PSNP.java trunk/src/lib/objects/FloatInt.java trunk/src/lib/objects/PETLocation.java trunk/src/lib/objects/FloatPair.java trunk/src/lib/objects/Aberation_SNP.java trunk/src/lib/objects/PETRead.java trunk/src/lib/objects/SETLocation.java trunk/src/lib/objects/Aberation_Deletion.java trunk/src/lib/objects/ReducedAlignedRead.java trunk/src/lib/objects/MAQouter.java trunk/src/lib/objects/Aberation_Insertion.java trunk/src/lib/Chromosome.java trunk/src/lib/StatisticsTools.java trunk/src/lib/Utilities.java trunk/src/lib/Constants.java trunk/src/lib/Error_handling trunk/src/lib/Error_handling/UnexpectedCharacterException.java trunk/src/lib/Error_handling/CommandLineProcessingException.java trunk/src/lib/Error_handling/OverflowException.java trunk/src/lib/Error_handling/UnexpectedResultException.java trunk/src/lib/Error_handling/DoesNotMatchException.java trunk/src/lib/Error_handling/GenericProcessingException.java trunk/src/lib/Error_handling/CanNotConnectException.java trunk/src/lib/FloatingPoint.java trunk/src/lib/ReducedAlignedReads.java trunk/src/lib/BitOperations.java trunk/src/lib/analysisTools trunk/src/lib/analysisTools/Exon_Junction_Map.java trunk/src/lib/analysisTools/CoreFunctions.java trunk/src/lib/analysisTools/Exon_Overlap.java trunk/src/lib/analysisTools/Process_SNPs.java trunk/src/lib/analysisTools/Transcript_Bias.java trunk/src/lib/analysisTools/Process_Exons.java trunk/src/lib/Ensembl.java trunk/src/lib/CommandLine.java trunk/src/lib/Coverage.java trunk/src/lib/ioInterfaces trunk/src/lib/ioInterfaces/MAQJunctionMapIterator.java trunk/src/lib/ioInterfaces/ElandExtUtilities.java trunk/src/lib/ioInterfaces/BowtieIterator.java trunk/src/lib/ioInterfaces/BedIterator.java trunk/src/lib/ioInterfaces/ExonerateIterator.java trunk/src/lib/ioInterfaces/FileOut.java trunk/src/lib/ioInterfaces/MultiMemberGZIPInputStream.java trunk/src/lib/ioInterfaces/FastaIterator.java trunk/src/lib/ioInterfaces/BedGraphWriter.java trunk/src/lib/ioInterfaces/GSC_Aberation_Iterator.java trunk/src/lib/ioInterfaces/VulgarIterator.java trunk/src/lib/ioInterfaces/SnpIterator.java trunk/src/lib/ioInterfaces/Log_Buffer.java trunk/src/lib/ioInterfaces/PushBackIteratorWrapper.java trunk/src/lib/ioInterfaces/GffIterator.java trunk/src/lib/ioInterfaces/PSNPwriter.java trunk/src/lib/ioInterfaces/ElandExtIterator.java trunk/src/lib/ioInterfaces/MapviewMAQIterator.java trunk/src/lib/ioInterfaces/Wigwriter.java trunk/src/lib/ioInterfaces/AceWriter.java trunk/src/lib/ioInterfaces/MAQmapIterator.java trunk/src/lib/ioInterfaces/Bedwriter.java trunk/src/lib/ioInterfaces/MapviewMAQPETIterator.java trunk/src/lib/ioInterfaces/PSNPIterator.java trunk/src/lib/ioInterfaces/Generic_AlignRead_Iterator.java trunk/src/lib/ioInterfaces/AlignedReadsIterator.java trunk/src/lib/ioInterfaces/SliderIterator.java trunk/src/lib/ioInterfaces/ElandIterator.java trunk/src/lib/Histogram.java trunk/src/projects trunk/src/projects/findFeatures trunk/src/projects/findFeatures/FindFeatures.java trunk/src/projects/findPeaks trunk/src/projects/findPeaks/Distribution.java trunk/src/projects/findPeaks/filewriters trunk/src/projects/findPeaks/filewriters/RegionWriter.java trunk/src/projects/findPeaks/filewriters/PeakWriter.java trunk/src/projects/findPeaks/PeakDataSetParent.java trunk/src/projects/findPeaks/FPConstants.java trunk/src/projects/findPeaks/tests trunk/src/projects/findPeaks/tests/test_linear_regressionPerpendicular.java trunk/src/projects/findPeaks/tests/test_linear_regression.java trunk/src/projects/findPeaks/FindPeaks.java trunk/src/projects/findPeaks/PeakLocator.java trunk/src/projects/findPeaks/FP_Output.java trunk/src/projects/findPeaks/Functions.java trunk/src/projects/findPeaks/objects trunk/src/projects/findPeaks/objects/PeakStats.java trunk/src/projects/findPeaks/objects/Peakdesc.java trunk/src/projects/findPeaks/objects/PeakPairIdx.java trunk/src/projects/findPeaks/objects/SaturationDataHolder.java trunk/src/projects/findPeaks/objects/Map_f.java trunk/src/projects/findPeaks/objects/MinPeakDesc.java trunk/src/projects/findPeaks/objects/Parameters.java trunk/src/projects/findPeaks/objects/Map_i.java trunk/src/projects/findPeaks/objects/SeqStore.java trunk/src/projects/findPeaks/objects/PairDistance.java trunk/src/projects/findPeaks/objects/LinearRegressionPerpendicular.java trunk/src/projects/findPeaks/objects/MapStore.java trunk/src/projects/findPeaks/objects/LinearRegression.java trunk/src/projects/findPeaks/objects/PeakStore.java trunk/src/projects/findPeaks/PeakDataSetChild.java trunk/src/projects/findPeaks/RFunctions.java trunk/src/projects/findPeaks/FDR trunk/src/projects/findPeaks/FDR/LanderWatermanTheory.java trunk/src/projects/findPeaks/FDR/MC_Simulation.java trunk/src/projects/findPeaks/FDR/ApplyControl.java trunk/src/projects/findPeaks/FDR/ApplyCompare.java trunk/src/projects/findPeaks/DuplicateFiltering.java trunk/src/projects/findPeaks/PeakLocatorSaturation.java trunk/src/projects/maq_utilities trunk/src/projects/maq_utilities/ReadsUsed.java trunk/src/projects/maq_utilities/objects trunk/src/projects/maq_utilities/objects/ExonBoundaries.java trunk/src/projects/maq_utilities/objects/GeneMap.java trunk/src/projects/maq_utilities/objects/Exonboundary.java trunk/src/projects/genomeViewer trunk/src/projects/genomeViewer/AlignSlice.java trunk/src/fileUtilities trunk/src/fileUtilities/CombineFiles.java trunk/src/fileUtilities/BowtieToBedFormat.java trunk/src/fileUtilities/RegionToBed.java trunk/src/fileUtilities/MapHeaderInfo.java trunk/src/fileUtilities/SeparateReads.java trunk/src/fileUtilities/MaqToReadFormat.java trunk/src/fileUtilities/SortFiles.java trunk/src/fileUtilities/ConvertToAce.java trunk/src/fileUtilities/ConvertToBed.java trunk/src/fileUtilities/MaqPetToBedFormat.java trunk/src/fileUtilities/RegionToAberations.java trunk/src/transcriptome_analysis trunk/src/transcriptome_analysis/Genome_Alignment trunk/src/transcriptome_analysis/Genome_Alignment/GenomicAlignmentAnalysis.java trunk/src/transcriptome_analysis/Genome_Alignment/TranscriptBiasAnalysis.java trunk/src/transcriptome_analysis/Transcriptome_Alignment trunk/src/transcriptome_analysis/Transcriptome_Alignment/Transcript_analysis.java trunk/src/transcriptome_analysis/SNP_Detection trunk/src/transcriptome_analysis/SNP_Detection/SNPAnalysis.java trunk/src/transcriptome_analysis/SNP_Detection/evaluate_snps.java trunk/src/transcriptome_analysis/SNP_Detection/PSNPAnalysisPipeline.java trunk/testdata trunk/testdata/22.test.eland trunk/classes trunk/build.xml trunk Révision 1325 extraite. Finally, the build: embryo@ubuntu:~$ cd trunk embryo@ubuntu:~/trunk$ ant fpsuite Buildfile: build.xml cleanfp: initfp: [mkdir] Created dir: /home/embryo/trunk/jars/fp4 compile: [javac] Compiling 137 source files to /home/embryo/trunk/classes FindPeaks: [mkdir] Created dir: /home/embryo/trunk/tmp [jar] Building jar: /home/embryo/trunk/jars/fp4/FindPeaks.jar [delete] Deleting directory /home/embryo/trunk/tmp SeparateReads: [mkdir] Created dir: /home/embryo/trunk/tmp [jar] Building jar: /home/embryo/trunk/jars/fp4/SeparateReads.jar [delete] Deleting directory /home/embryo/trunk/tmp SortFiles: [mkdir] Created dir: /home/embryo/trunk/tmp [jar] Building jar: /home/embryo/trunk/jars/fp4/SortFiles.jar [delete] Deleting directory /home/embryo/trunk/tmp GenomeViewer: [mkdir] Created dir: /home/embryo/trunk/tmp [jar] Building jar: /home/embryo/trunk/jars/fp4/AlignSlice.jar [delete] Deleting directory /home/embryo/trunk/tmp ConvertToBed: [mkdir] Created dir: /home/embryo/trunk/tmp [jar] Building jar: /home/embryo/trunk/jars/fp4/ConvertToBed.jar [delete] Deleting directory /home/embryo/trunk/tmp MaqPetToBed: [mkdir] Created dir: /home/embryo/trunk/tmp [jar] Building jar: /home/embryo/trunk/jars/fp4/MaqPetToBed.jar [delete] Deleting directory /home/embryo/trunk/tmp buildfp: fptestdata: [copy] Copying 1 file to /home/embryo/trunk/jars/fp4 changelog: [copy] Copying 1 file to /home/embryo/trunk/jars fpsuite: BUILD SUCCESSFUL Total time: 3 seconds And... now going home. *Heather 14:44, 6 July 2009 (EDT): Heather 14:40, 6 July 2009 (EDT):