Etchevers:Notebook/STRA6 in eye development/2009/06/30: Difference between revisions

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==Title==
==Building [http://vancouvershortr.wiki.sourceforge.net/FindPeaks4 FindPeaks]==
This entry will describe today's efforts.
''I hate the way OWW will automatically log you out after a finite, arbitrary amount of time and NOT SAVE DRAFTS. Or at least I don't know where to find them. Make sure to '''apt-get install subversion''' first.''


:~$ '''svn co http://vancouvershortr.svn.sourceforge.net/svnroot/vancouvershortr/trunk'''
U    trunk/Changelog.txt
U    trunk/src/lib/analysisTools/Exon_Overlap.java
U    trunk/src/lib/analysisTools/Process_Exons.java
U    trunk/src/lib/Ensembl.java
D    trunk/src/projects/findFeatues
A    trunk/src/projects/findFeatures
A    trunk/src/projects/findFeatures/FindFeatures.java
U    trunk/src/projects/findPeaks/filewriters/PeakWriter.java
U    trunk/src/projects/findPeaks/PeakDataSetParent.java
U    trunk/src/projects/findPeaks/FPConstants.java
U    trunk/src/projects/findPeaks/FindPeaks.java
U    trunk/src/projects/findPeaks/objects/SaturationDataHolder.java
U    trunk/src/projects/findPeaks/objects/Parameters.java
U    trunk/src/projects/findPeaks/objects/LinearRegressionPerpendicular.java
U    trunk/src/projects/findPeaks/PeakDataSetChild.java
U    trunk/src/projects/findPeaks/FDR/MC_Simulation.java
U    trunk/src/projects/findPeaks/FDR/ApplyControl.java
U    trunk/src/fileUtilities/MaqPetToBedFormat.java
U    trunk/src/transcriptome_analysis/SNP_Detection/PSNPAnalysisPipeline.java
U    trunk/build.xml
Checked out revision 1309.
:~$ '''ls'''
calib-36.dat  Documents        hg18      maqview  Pictures  Templates  Videos
Desktop      examples.desktop  maq-0.7.1  Music    Public    trunk
:~$ ant fpsuite
Buildfile: build.xml does not exist!
Build failed
''(Oops. One was forewarned.)''
:~$ '''cd trunk'''
:~/trunk$ ls
build.xml  Changelog.txt  classes  jars  lib  src  testdata
$ '''ant fpsuite'''
Buildfile: build.xml
cleanfp:
initfp:
    [mkdir] Created dir: /home/heather/trunk/jars/fp4
compile:
    [javac] Compiling 137 source files to /home/heather/trunk/classes
FindPeaks:
    [mkdir] Created dir: /home/heather/trunk/tmp
      [jar] Building jar: /home/heather/trunk/jars/fp4/FindPeaks.jar
  [delete] Deleting directory /home/heather/trunk/tmp
SeparateReads:
    [mkdir] Created dir: /home/heather/trunk/tmp
      [jar] Building jar: /home/heather/trunk/jars/fp4/SeparateReads.jar
  [delete] Deleting directory /home/heather/trunk/tmp
SortFiles:
    [mkdir] Created dir: /home/heather/trunk/tmp
      [jar] Building jar: /home/heather/trunk/jars/fp4/SortFiles.jar
  [delete] Deleting directory /home/heather/trunk/tmp
GenomeViewer:
    [mkdir] Created dir: /home/heather/trunk/tmp
      [jar] Building jar: /home/heather/trunk/jars/fp4/AlignSlice.jar
  [delete] Deleting directory /home/heather/trunk/tmp
ConvertToBed:
    [mkdir] Created dir: /home/heather/trunk/tmp
      [jar] Building jar: /home/heather/trunk/jars/fp4/ConvertToBed.jar
  [delete] Deleting directory /home/heather/trunk/tmp
MaqPetToBed:
    [mkdir] Created dir: /home/heather/trunk/tmp
      [jar] Building jar: /home/heather/trunk/jars/fp4/MaqPetToBed.jar
  [delete] Deleting directory /home/heather/trunk/tmp
buildfp:
fptestdata:
    [copy] Copying 1 file to /home/heather/trunk/jars/fp4
changelog:
    [copy] Copying 1 file to /home/heather/trunk/jars
fpsuite:
BUILD SUCCESSFUL
Total time: 7 seconds
''I've elided the few attempts where I messed up the pathnames, but here is the last one and I don't see why it can't find MaqPetToBedFormat, as the fileUtilities folder contains:''
BowtieToBedFormat.java  MapHeaderInfo.java      RegionToBed.java
CombineFiles.java      '''MaqPetToBedFormat.java'''  SeparateReads.java
ConvertToAce.java      MaqToReadFormat.java    SortFiles.java
ConvertToBed.java      RegionToAberations.java
:~$ '''time java -Xmx4G ~/trunk/src/fileUtilities/MaqPetToBedFormat -output ~/maq-0.7.1/PetToBeds/ -name PAX6 -input ~/maq-0.7.1/outdirPAX6/allPAX6.map -maq_read_size 128 -bridge'''
Exception in thread "main" java.lang.NoClassDefFoundError: /home/heather/trunk/src/fileUtilities/MaqPetToBedFormat
Caused by: java.lang.ClassNotFoundException: .home.heather.trunk.src.fileUtilities.MaqPetToBedFormat
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:336)
Could not find the main class: /home/heather/trunk/src/fileUtilities/MaqPetToBedFormat. Program will exit.
real 0m0.194s
user 0m0.140s
sys 0m0.020s
Since I don't know what a class is, I can't fix the problem. I also wonder if I can use single-end tags rather than paired-end, and what it will do with the bridge flag if so. Then again, it seems like anything that hasn't been paired (everything in principle) will end up in :
* "paired(map)-SET.bed.gz: this bed file contains all reads that could not be paired - either because their mate pair was unmappable by Maq, or because their mate pair was below the minimum quality filter." Write Anthony and ask for help here.
*'''[[User:Etchevers|Heather]] 02:48, 30 June 2009 (EDT)''':


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Revision as of 23:48, 29 June 2009

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Building FindPeaks

I hate the way OWW will automatically log you out after a finite, arbitrary amount of time and NOT SAVE DRAFTS. Or at least I don't know where to find them. Make sure to apt-get install subversion first.

~$ svn co http://vancouvershortr.svn.sourceforge.net/svnroot/vancouvershortr/trunk

U trunk/Changelog.txt U trunk/src/lib/analysisTools/Exon_Overlap.java U trunk/src/lib/analysisTools/Process_Exons.java U trunk/src/lib/Ensembl.java D trunk/src/projects/findFeatues A trunk/src/projects/findFeatures A trunk/src/projects/findFeatures/FindFeatures.java U trunk/src/projects/findPeaks/filewriters/PeakWriter.java U trunk/src/projects/findPeaks/PeakDataSetParent.java U trunk/src/projects/findPeaks/FPConstants.java U trunk/src/projects/findPeaks/FindPeaks.java U trunk/src/projects/findPeaks/objects/SaturationDataHolder.java U trunk/src/projects/findPeaks/objects/Parameters.java U trunk/src/projects/findPeaks/objects/LinearRegressionPerpendicular.java U trunk/src/projects/findPeaks/PeakDataSetChild.java U trunk/src/projects/findPeaks/FDR/MC_Simulation.java U trunk/src/projects/findPeaks/FDR/ApplyControl.java U trunk/src/fileUtilities/MaqPetToBedFormat.java U trunk/src/transcriptome_analysis/SNP_Detection/PSNPAnalysisPipeline.java U trunk/build.xml Checked out revision 1309.

~$ ls

calib-36.dat Documents hg18 maqview Pictures Templates Videos Desktop examples.desktop maq-0.7.1 Music Public trunk

~$ ant fpsuite

Buildfile: build.xml does not exist! Build failed

(Oops. One was forewarned.)

~$ cd trunk
~/trunk$ ls

build.xml Changelog.txt classes jars lib src testdata

$ ant fpsuite Buildfile: build.xml

cleanfp:

initfp: 

   [mkdir] Created dir: /home/heather/trunk/jars/fp4

compile: 

   [javac] Compiling 137 source files to /home/heather/trunk/classes

FindPeaks: 

   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/FindPeaks.jar
  [delete] Deleting directory /home/heather/trunk/tmp

SeparateReads: 

   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/SeparateReads.jar
  [delete] Deleting directory /home/heather/trunk/tmp

SortFiles: 

   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/SortFiles.jar
  [delete] Deleting directory /home/heather/trunk/tmp

GenomeViewer: 

   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/AlignSlice.jar
  [delete] Deleting directory /home/heather/trunk/tmp

ConvertToBed: 

   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/ConvertToBed.jar
  [delete] Deleting directory /home/heather/trunk/tmp

MaqPetToBed: 

   [mkdir] Created dir: /home/heather/trunk/tmp
     [jar] Building jar: /home/heather/trunk/jars/fp4/MaqPetToBed.jar
  [delete] Deleting directory /home/heather/trunk/tmp

buildfp:

fptestdata: 

    [copy] Copying 1 file to /home/heather/trunk/jars/fp4

changelog: 

    [copy] Copying 1 file to /home/heather/trunk/jars

fpsuite:

BUILD SUCCESSFUL Total time: 7 seconds

I've elided the few attempts where I messed up the pathnames, but here is the last one and I don't see why it can't find MaqPetToBedFormat, as the fileUtilities folder contains:

BowtieToBedFormat.java MapHeaderInfo.java RegionToBed.java CombineFiles.java MaqPetToBedFormat.java SeparateReads.java ConvertToAce.java MaqToReadFormat.java SortFiles.java ConvertToBed.java RegionToAberations.java


~$ time java -Xmx4G ~/trunk/src/fileUtilities/MaqPetToBedFormat -output ~/maq-0.7.1/PetToBeds/ -name PAX6 -input ~/maq-0.7.1/outdirPAX6/allPAX6.map -maq_read_size 128 -bridge

Exception in thread "main" java.lang.NoClassDefFoundError: /home/heather/trunk/src/fileUtilities/MaqPetToBedFormat Caused by: java.lang.ClassNotFoundException: .home.heather.trunk.src.fileUtilities.MaqPetToBedFormat at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:323) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:268) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:336) Could not find the main class: /home/heather/trunk/src/fileUtilities/MaqPetToBedFormat. Program will exit.

real 0m0.194s user 0m0.140s sys 0m0.020s

Since I don't know what a class is, I can't fix the problem. I also wonder if I can use single-end tags rather than paired-end, and what it will do with the bridge flag if so. Then again, it seems like anything that hasn't been paired (everything in principle) will end up in :

  • "paired(map)-SET.bed.gz: this bed file contains all reads that could not be paired - either because their mate pair was unmappable by Maq, or because their mate pair was below the minimum quality filter." Write Anthony and ask for help here.
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