BIRCHv3.00

From Bioinformatics.Org Wiki

Jump to: navigation, search

Contents

Generate Download Statistics

First attempt using awstats.pl

There wasn't enough support from IST on this, so I decided to write a simple backend and put it on a Bit server. See BIRCH Download Stats

Getbirch Wizard

Convert menus to PCD

  1. Convert BIRCH core menus
  2. Need to refactor paths to files for Help buttons in menus
  3. Add empty PCD directories to local-generic/dat
  4. Update documentation to show how to create PCD menus. Make sure to keep the GDE documentation around as a deprecated package

Installation and Uninstallation

Move GetBIRCH Python scripts to install-scripts

  1. Move Python scripts to install-scripts
  2. Change GetBIRCH to look for them there
  3. Change birchconfig to look for them there
  4. Make sure we don't lose features that were added to the .sh scripts

birchadmin

birchadmin is a birch system administration tool.

bldna

blprotein

Output to blnfetch, blpfetch

blncbi

blastcl3 - replace with BLAST+

blastcl3 is now deprecated, in favor of the BLAST+ tools. Apparently, all BLAST+ tools have a -remote commandline switch that sends the search to NCBI, instead of running it locally. blastcl3 requires a socket that remains connected to NCBI for the duration of the search, whereas BLAST+ does not.

Please see http://1.usa.gov/xbErSV

New BLAST+ PCD Menus

SEQUIN

Upgrade to latest version
Updated to Version 13.70 on linux-x86_64 and MacOSX. NCBI appears to no longer be supporting Solaris. Consequently, the solaris-sparc and solaris-amd64 binaries have been updated to Version 13.05, the latest version for these platforms.

blnalign, blpalign

Break out multiple alignment tasks from bldna and blprotein into new BioLegato instances, blnalign and blpalign, respectively. This improves the object-oriented nature of the various BioLegatos. In particular, it makes it harder to do, for example, phylogeny tasks on sets of unaligned sequences, or to feed sequences with gaps into sequence programs that expect no gaps.

  1. blnalign - extract menus for viewing alignments, phylogeny, removal of gaps
  2. blpalign - extract menus for viewing alignments, phylogeny, removal of gaps
  3. bldna - remove menus for viewing alignments, phylogeny, removal of gaps; alignment progs. call blnalign
  4. blprotein - remove menus for viewing alignments, phylogeny, removal of gaps; alignment progs. call blpalign
  5. birch - add launchers for blpalign, blnalign
  6. revise install scripts to add blpalign and blnalign sections to local.
  1. birchdb - add entries for blnalign and blpalign; change entries for other programs to reflect whether they are run in blnalign or blpalign.
  2. mrtrans - remove from bldna, blprotein and blnalign. Revise menu in blpalign so that it exports the protein alignment, and the only parameter set is the name of the unaligned DNA file.
  3. Revise tutorials
  4. Edit menus - change CopyOut and PasteIn to use .blnalign_clipboard and .blpalign_clipboard; modify Sort and Extract menus to use blnalign and blpalign.
  5. File-->New Window
  6. Update the BioLegato Edit help page to list .blnalign_clipboard and .blpalign_clipboard. While we're there, also mention that Sort is, in fact implemented.
  7. weblogo - Apparently, weblogo requires ghostscript to generate all file formats except for eps. Although gs seems to be standard on Linux, it is not on OSX. With the default settings, blpalign/blnalign will not produce an output window. Solution: Make EPS the default format. weblogo.py doesn't require ghostscript for EPS, so this will work on all configurations. The other choices (PDF, PNG, JPEG) will work if ghostscript is installed.

Binaries


linux-x86_64
linux-intel
osx-x86_64
solaris-sparc
solaris-amd64
BLAST+
v2.2.30
v2.2.30
v2.2.30
 v2.2.27

requires libzo2.so.2

v2.2.27
FASTA3
36.3.6
36.3.7a
36.3.6
36.3.6

Database search programs reverted to fasta35, fastx35, fasty35 tfastx35 tfasty35 because of execution errors

36.3.6
Database search programs reverted to fasta35, fastx35, fasty35 tfastx35 tfasty35 because of execution errors
Sequin
13.70
13.05, the latest version for these platforms.
13.70
13.05, the latest version for these platforms.
13.05, the latest version for these platforms.
t_coffee
11.8
v8.14
v8.14

(later versions either won't compile on albacore or give error messages)

8.14

later versions not tried

8.14
later versions not tried
Phylip
3.69
3.69
3.69
3.69
3.69
Personal tools
Namespaces
Variants
Actions
wiki navigation
Toolbox