V2.0.0 release

Shipping process

[sboisver12@colosse1 ray]$ ./scripts/ShipProduct.sh v2.0.0
Welcome to Ray Technologies.
Today we ship a product.

Assembling product parts
Cloning /home/sboisver12/git-clones/ray
Cloning /home/sboisver12/git-clones/RayPlatform
Cloning /home/sboisver12/git-clones/RayPlatform-example
Creating product releases.
.tar.bz2
.tar.gz
.zip
.tar.xz
The product was shipped to /home/sboisver12/ProductReleases/Ray-v2.0.0

• submit the "méta-Ray" paper Under review
• Peak for seeds https://github.com/sebhtml/ray/issues/47
• FAQ https://github.com/sebhtml/ray/issues/56 2012-06-22
• new multiplicator for read fetcher. (2 -> 1.5) 2012-06-22
• run regression tests (+backup on colosse) 2012-06-22
• run unit tests 2012-06-20
• check version in Makefile 2012-06-20
• ./Ray -help > MANUAL_PAGE.txt 2012-06-20
• compile with make 2012-06-20
• compile with cmake 2012-06-20
• git tag vx.y.z 2012-06-23
• git checkout tag, 2012-06-23
• do a tar.bz2, compile it (make + make install) and test it 2012-06-23
• upload the tarball on sf 2012-06-23
• update the web site (download + manual) 2012-06-23
• post an email on the list including changes (dump-changes) 2012-06-23
• update the seqanswer thread 2012-06-23

v2.0.0

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 coli.Ray & 71 & 66 & 4582298 & 64539 & 126417 &  222309 &  0.9899 & 4 & 0 & 7 & 4 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 coli-interleaved.Ray & 73 & 68 & 4593274 & 62921 & 114742 &  222309 &  0.9902 & 4 & 0 & 7 & 4 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 ecoli-MiSeq.Ray & 86 & 82 & 4583637 & 53298 & 95817 &  269165 &  0.9852 & 1 & 1 & 23 & 43 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 L1-L3.Ray & 8 & 1 & 4653127 & 581640 & 1249896 &  1524225 &  1.0000 & 2 & 0 & 47 & 20 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 multiple-peaks.Ray & 5 & 4 & 882644 & 176528 & 614024 &  614024 &  0.9998 & 2 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pg2.Ray & 6 & 6 & 871450 & 145241 & 612159 &  612159 &  0.9976 & 0 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 phix.Ray & 1 & 1 & 5386 & 5386 & 5386 &  5386 &  1.0000 & 0 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pseudomonas-interleaved-bz2.Ray & 74 & 56 & 6224418 & 84113 & 233788 &  572438 &  0.9964 & 3 & 0 & 1 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pseudomonas-p.Ray & 103 & 99 & 6220001 & 60388 & 248130 &  580140 &  0.9955 & 0 & 1 & 45 & 2 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pseudomonas-p-bz2-gz.Ray & 103 & 99 & 6219750 & 60385 & 248130 &  580140 &  0.9955 & 0 & 1 & 45 & 2 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pseudomonas-s.Ray & 1946 & 1946 & 6032720 & 3100 & 4781 &  29440 &  0.9628 & 1 & 0 & 1 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept.Ray & 104 & 97 & 2000711 & 19237 & 36431 &  128039 &  0.9843 & 0 & 1 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-200.Ray & 104 & 97 & 2000650 & 19237 & 36431 &  128039 &  0.9845 & 0 & 1 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-300.Ray & 71 & 61 & 2008075 & 28282 & 55479 &  182993 &  0.9839 & 0 & 0 & 1 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-amos.Ray & 104 & 97 & 2000682 & 19237 & 36431 &  128039 &  0.9843 & 0 & 1 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-bz2.Ray & 105 & 98 & 2001352 & 19060 & 36431 &  128039 &  0.9845 & 0 & 1 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-interleaved.Ray & 104 & 97 & 2000718 & 19237 & 36431 &  128039 &  0.9843 & 0 & 1 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-interleaved-bz2.Ray & 104 & 97 & 2000650 & 19237 & 36431 &  128039 &  0.9845 & 0 & 1 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-simulated-errors.Ray & 99 & 82 & 1997709 & 20178 & 37594 &  127936 &  0.9856 & 0 & 0 & 1 & 0 \\

Ray 7102b16f1f282a0003f9982b42a3a744d9bffe59

validation with MUMMER:

misassembledContigs contains small indels too, which are not really a problem at that scale.

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 coli.Ray & 66 & 60 & 4593129 & 69592 & 134245 &  222309 &  0.9924 & 5 & 0 & 36 & 6 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 coli-interleaved.Ray & 68 & 61 & 4599008 & 67632 & 134245 &  222309 &  0.9934 & 4 & 0 & 36 & 6 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 ecoli-MiSeq.Ray & 92 & 83 & 4584978 & 49836 & 95817 &  268554 &  0.9850 & 2 & 0 & 33 & 25 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 L1-L3.Ray & 8 & 4 & 4646253 & 580781 & 1090091 &  1509013 &  0.9857 & 5 & 0 & 69 & 47 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 multiple-peaks.Ray & 2 & 1 & 873283 & 436641 & 815918 &  815918 &  0.9999 & 2 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pg2.Ray & 6 & 6 & 874820 & 145803 & 614763 &  614763 &  0.9984 & 0 & 0 & 1 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 phix.Ray & 1 & 1 & 5386 & 5386 & 5386 &  5386 &  1.0000 & 0 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pseudomonas-interleaved-bz2.Ray & 77 & 56 & 6226244 & 80860 & 183096 &  572252 &  0.9962 & 2 & 1 & 1 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pseudomonas-p.Ray & 1666 & 1666 & 6051984 & 3632 & 5894 &  48599 &  0.9659 & 1 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pseudomonas-p-bz2-gz.Ray & 1661 & 1661 & 6053235 & 3644 & 5917 &  48599 &  0.9661 & 2 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 pseudomonas-s.Ray & 1675 & 1675 & 6053567 & 3614 & 5872 &  48599 &  0.9662 & 1 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept.Ray & 0 & 0 &  &  &  &   &  0.0000 &  &  &  &  \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-200.Ray & 95 & 92 & 2004757 & 21102 & 39231 &  128046 &  0.9860 & 0 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-300.Ray & 78 & 69 & 2017890 & 25870 & 48703 &  183041 &  0.9945 & 0 & 0 & 1 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-amos.Ray & 95 & 92 & 2004109 & 21095 & 39231 &  128046 &  0.9854 & 0 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-bz2.Ray & 95 & 92 & 2004109 & 21095 & 39231 &  128046 &  0.9854 & 0 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-interleaved.Ray & 95 & 92 & 2004109 & 21095 & 39231 &  128046 &  0.9854 & 0 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-interleaved-bz2.Ray & 95 & 92 & 2004328 & 21098 & 39231 &  128046 &  0.9855 & 0 & 0 & 0 & 0 \\

        %  & numberOfContigs &scaffolds & bases & meanSize  & n50  & max   & coverage   & misassembledContigs & misassembledScaffolds & mismatches & indels
 strept-simulated-errors.Ray & 96 & 81 & 2005869 & 20894 & 37594 &  127941 &  0.9884 & 0 & 0 & 0 & 0 \\