The second beta release of Pregap4 has now been placed in the LMB ftp site.
The changes are entirely to the tcl script components and so people
who have downloaded the beta-1 release need only to fetch (42K):
The full release is operating system specific (as it contains several
binary components) and can be fetched from:
A brief list of changes from the beta-1 release follows.
* SP value (sequencing vector primer site) can now be entered as two
numbers separated by a /. Eg 41/-24. This specifies both forward and
reverse primer site values. Requires PR (primer type) to be known.
* Improved error messages, report generation, and filename usage.
* The config file is now easier to read. The "module" command is no
longer needed (manual configuration) as the namespace is taken from
the config section.
* The *_use_sample_name configurations are now part of the init.pm
module instead of global variables.
* File of filenames from remote directories now works better - we assume
that all filenames listed within it are pathnames relative to the
directory containing the fofn.
* Loading a new config file with the configure dialogue not
displayed (in separate window mode) was producing a tk error.
* Editing the "files" list box now actually updates the list of files to
* Added a Cap3 module.
* The report mechanism was displaying reports for modules no longer
* The <fofn>.log file now includes 'file history'. Eg:
02ap1a.exp (EXP) <- 02ap1a.scf (SCF) <- Sample01.abi (ABI)
* Greatly improved error detection and recovery for all modules.
James Bonfield (jkb at mrc-lmb.cam.ac.uk) Tel: 01223 402499 Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/