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* Added built tools to the SVN.

* Modified ANT scripts for full support of client, viewer and server versions.
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Thilo.Muth Thilo.Muth
Thilo.Muth authored and Thilo.Muth committed Aug 20, 2014
1 parent b12093d commit 06863dc730405e742c14845f82a900e622526b23
Showing with 1,055,681 additions and 35 deletions.
  1. +17 −17 .project
  2. +3 −4 built/README_Client.txt
  3. +3 −4 built/README_Server.txt
  4. +2 −0 built/clearfolders.sh
  5. +5 −0 built/fasta/DBTools/Changes
  6. +26 −0 built/fasta/DBTools/MANIFEST
  7. +31 −0 built/fasta/DBTools/META.yml
  8. +21 −0 built/fasta/DBTools/Makefile.PL
  9. +34 −0 built/fasta/DBTools/README
  10. +252 −0 built/fasta/DBTools/cgi/cgiUniprotEntry.pl
  11. +63 −0 built/fasta/DBTools/lib/InSilicoSpectro/Databanks.pm
  12. +360 −0 built/fasta/DBTools/lib/InSilicoSpectro/Databanks/DBEntry.pm
  13. +520 −0 built/fasta/DBTools/lib/InSilicoSpectro/Databanks/DBEntryUniprot.pm
  14. +346 −0 built/fasta/DBTools/scripts/fasta-decoy.pl
  15. +503 −0 built/fasta/DBTools/scripts/fasta-shuffle-notryptic.pl
  16. +276 −0 built/fasta/DBTools/scripts/ncbinr2phenyxfasta.pl
  17. +183 −0 built/fasta/DBTools/scripts/uniprotdat2fasta.pl
  18. +9 −0 built/fasta/DBTools/t/00-load.t
  19. +30 −0 built/fasta/DBTools/t/DBEntry.t
  20. +432 −0 built/fasta/DBTools/t/DBEntryUniprot.t
  21. +48 −0 built/fasta/DBTools/t/DBUniprot.t
  22. +1,587 −0 built/fasta/DBTools/t/insilicodef-test.xml
  23. +8 −0 built/fasta/DBTools/t/pod-coverage.t
  24. +6 −0 built/fasta/DBTools/t/pod.t
  25. +52 −0 built/fasta/DBTools/t/same-aacompo.pl
  26. +47 −0 built/fasta/DBTools/t/same-length.pl
  27. +101 −0 built/fasta/DBTools/t/same-pept-count.pl
  28. +46 −0 built/fasta/fastaformat.sh
  29. BIN built/fasta/indexfasta.jar
  30. +669 −0 built/sql/metaprot.sql
  31. +1,049,858 −0 built/sql/taxonomy.sql
  32. +85 −0 client_export.xml
  33. +7 −5 server_export.xml
  34. +2 −0 src/conf/client-settings_default.txt
  35. +5 −0 src/conf/connection-settings_default.txt
  36. +39 −0 src/conf/server-settings.txt
  37. +5 −5 viewer_export.xml
View
@@ -1,17 +1,17 @@
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>MetaProteomeAnalyzer</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.jdt.core.javanature</nature>
</natures>
</projectDescription>
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>MetaProteomeAnalyzer</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.jdt.core.javanature</nature>
</natures>
</projectDescription>
View
@@ -22,12 +22,11 @@
The default value is set to -Xmx1500m (for 1500 MB RAM) in this case.
===============================
MetaProteomeAnalyzer Web Page
MPA Client Installation
===============================
For updated information and documentation (including wiki) about the MetaProteomeAnalyzer project please visit:
http://meta-proteome-analyzer.googlecode.com
For more information and documentation about the MPA Client Installation please visit:
https://code.google.com/p/meta-proteome-analyzer/wiki/Client_Installation
=========
View
@@ -19,12 +19,11 @@
The default value is set to -Xmx2048m (for 2 GB RAM) in this case.
===============================
MetaProteomeAnalyzer Web Page
MPA Server Installation
===============================
For updated information and documentation (including wiki) about the MetaProteomeAnalyzer project please visit:
http://meta-proteome-analyzer.googlecode.com
For more information and documentation about the MPA Server Installation please visit:
https://code.google.com/p/meta-proteome-analyzer/wiki/Server_Installation
=========
View
@@ -1,3 +1,5 @@
#/bin/bash!
echo "Clearing folders..."
find /scratch/metaprot/data/transfer -type f -exec rm -f {} \;
find /scratch/metaprot/data/output -type f -exec rm -f {} \;
echo "Clearing folders finished."
@@ -0,0 +1,5 @@
Revision history for InSilicoSpectro-Databanks
0.01 Date/time
First version, released on an unsuspecting world.
@@ -0,0 +1,26 @@
Changes
MANIFEST
META.yml # Will be created by "make dist"
Makefile.PL
README
META.yml
Makefile.PL
README
cgi/cgiUniprotEntry.pl
lib/InSilicoSpectro/Databanks.pm
lib/InSilicoSpectro/Databanks/DBEntry.pm
lib/InSilicoSpectro/Databanks/DBEntryUniprot.pm
scripts/uniprotdat2fasta.pl
scripts/fasta-decoy.pl
scripts/fasta-shuffle-notryptic.pl
scripts/ncbinr2phenyxfasta.pl
t/DBEntry.t
t/DBEntryUniprot.t
t/DBUniprot.t
t/00-load.t
t/pod-coverage.t
t/pod.t
t/insilicodef-test.xml
t/same-pept-count.pl
t/same-length.pl
t/same-aacompo.pl
@@ -0,0 +1,31 @@
---
name: InSilicoSpectro-Databanks
version: 0.0.43
author:
- 'Alexandre Masselot <alexandre.masselot@genebio.com>'
abstract: 'parsing protein/nucleotides sequence databanks (fasta, uniprot...)'
license: lgpl
resources:
license: http://opensource.org/licenses/artistic-license.php
requires:
LWP::Simple: 0
Log::StdLog: 0
Object::InsideOut: 0
perl: 5.6.1
recommends:
Bio::Perl: 1.4
Bit::Vector: 0
InSilicoSpectro: 0
String::CRC: 0
provides:
InSilicoSpectro::Databanks:
file: lib/InSilicoSpectro/Databanks.pm
version: 0.0.43
InSilicoSpectro::Databanks::DBEntry:
file: lib/InSilicoSpectro/Databanks/DBEntry.pm
InSilicoSpectro::Databanks::DBEntryUniprot:
file: lib/InSilicoSpectro/Databanks/DBEntryUniprot.pm
generated_by: Module::Build version 0.2808
meta-spec:
url: http://module-build.sourceforge.net/META-spec-v1.2.html
version: 1.2
@@ -0,0 +1,21 @@
# Note: this file was auto-generated by Module::Build::Compat version 0.03
use ExtUtils::MakeMaker;
WriteMakefile
(
'PL_FILES' => {},
'INSTALLDIRS' => 'site',
'NAME' => 'InSilicoSpectro::Databanks',
'EXE_FILES' => [
'scripts/fasta-decoy.pl',
'scripts/fasta-shuffle-notryptic.pl',
'scripts/ncbinr2phenyxfasta.pl',
'scripts/uniprotdat2fasta.pl'
],
'VERSION_FROM' => './lib/InSilicoSpectro/Databanks.pm',
'PREREQ_PM' => {
'Log::StdLog' => 0,
'LWP::Simple' => 0,
'Object::InsideOut' => 0
}
)
;
View
@@ -0,0 +1,34 @@
NAME
InSilicoSpectro::Databanks - parsing protein/nucleotides sequence
databanks (fasta, uniprot...)
SYNOPSIS
$/="//\n"; while (<FDIN>){ my
$dbu=InSilicoSpectro::Databanks::DBEntryUniprot->new; $dbu->readDat($_);
my @tmp=$dbu->generateDerivedForms(); unless ( && @tmp){
$dbu->printFasta; $origSeq = $dbu->sequence; } foreach (@tmp){ if
($_->sequence ne $origSeq){ $_->printFasta; } } }
EXPORT
A list of functions that can be exported. You can delete this section if
you don't export anything, such as for a purely object-oriented module.
FUNCTIONS
AUTHOR
Alexandre Masselot, "<alexandre.masselot@genebio.com>"
BUGS
Please report any bugs or feature requests to
"bug-insilicospectro-databanks@rt.cpan.org", or through the web
interface at
<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=InSilicoSpectro-Databank
s>. I will be notified, and then you'll automatically be notified of
progress on your bug as I make changes.
ACKNOWLEDGEMENTS
COPYRIGHT & LICENSE
Copyright 2006 Alexandre Masselot, all rights reserved.
This program is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.
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