Thursday 11 November 2010

Bioscope 1.3 is a whopping 6.6 Gb!! Officially released for download

Downloading v 1.3 now. Gosh it is a whopping 6.6 Gb download.(270 Mb for v 1.21)
Not sure where the bloat comes from. Guessing it's example data, hope the server doesn't crash under the load. 
btw reason no. 5 for using Bioscope v 1.3 sounds quite flaky...


UPDATE: Argh. the md5sums match my download but I got this error
error [4462069.zip]:  start of central directory not found;
  zipfile corrupt.
  (please check that you have transferred or created the zipfile in the
  appropriate BINARY mode and that you have compiled UnZip properly)


UPDATE2: Finally unzipped the 6.6 Gb file in an xp box using 7zip (apparently linux zip is finicky for files > 4 Gb. )
Guess what's inside? tarred zip files. Oh what fun to transfer them back to a linux box!
BioScope-1.3-9.tar.gz           (Regular, application/x-compressed-tar) size 217743781  mode 0744
BioScope-1.3.rBS130-51653_20101021190735.examples.tar.gz                (Regular, application/x-compressed-tar) size 4206422209 mode 0744
BS130-resources.tar.gz          (Regular, application/x-compressed-tar) size 2632156337 mode 0744

UPDATE 2: 
ABI has updated the downloads to a more reasonable 
208Mb Nov 25 04:24 bioscope1.3.1installer_4464106.tar.gz
md5 checksum is b688a8ae7b620d7b2dc7f68c6ca41783
 
Dear Valued Customer,

It is with great pleasure and excitement that I announce the release and immediate availability of BioScope v1.3

BioScope, the modular SOLiD™ data analysis bioinformatics tool, is designed specifically to optimize the accuracy of your SOLiD™ colorspace data.  In addition to streamlining the construction and maintenance of your SOLiD™ pipelines, BioScope provides a simple web interface allowing non command line users the power of running sophisticated NGS data analysis.

SOLiD™ BioScope provides workflow applications including:
  • Improved MaxMapper Mapping and Pairing
  • BFAST integration
  • Improved SAET Accuracy Enhancement
  • Resequencing Pipelines
    • SNP/diBayes
    • Inversion
    • CNV
    • Small Indel
    • Large Indel
  • Whole Transcriptome
  • Fusion Transcript and Splicing Detection
  • Target Resequencing
  • Support for ChIPSeq
  • Support for Methyl Miner
  • Annotation and Reporting
  • Improved BAM file compatibility
  • Improved BioScope™ Users Guide

Additional details can be found at the following blog:

Also attached is an in-depth article about our new Target Resequencing pipeline in BioScope™.


Please coordinate with your IT admin, bioinformatician, lab manager, and PI to have BioScope v1.3 installed at your site.

To get your free copy of SOLiDBioScope please go to:

Please ensure that you have an activated account on solidsoftwaretools.comRupert.Yip@lifetech.com before downloading.  If you have problems downloading, please contact

If this is your first time installing BioScope, we strongly recommend working with the BioScope software installation team to ensure a proper installation and configuration of BioScope.  Please contact Rupert.Yip@lifetech.com to inquire about our free BioScope software installation services.

For information BioScope training please contact your local bioinformatics FAS or go to http://learn.appliedbiosystems.com/solid

2 comments:

  1. So after going through this nightmare.... does anything work ? Was it worth the pain ? Or did you have to quit midway ?

    Sorry for my "intrusive" questions, but I'm
    trying to decide if to follow in your path, or just buy a proven, trivial to install commercial software like ISAS.

    Thanks,
    Hans

    ReplyDelete
  2. Well, it seems improper for me to comment as I have no experience nor knowledge of what ISAS is. Would you care to elaborate on your experience?

    ReplyDelete

Datanami, Woe be me