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

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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.

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

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):


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