Run 1.1.0 1.2.0 delta

These are detailed notes on changes made between bioperl-release-1-1-0 and bioperl-run-release-1-2-0.

Bio::Factory::EMBOSS

Moving from bioperl-live CVS module

Bio::Tools::Run::Alignment::Blat

Moving to Bio::Tools::Run::Alignment Namespace

Some code cleanup to avoid warnings and insure filehandles are properly closed, etc

Bio::Tools::Run::Alignment::Clustalw

Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)

Allow phylip output format to be set

Make sure we cleanup tempfiles before each run

Make sure we've closed temporary file handles

Some changes to deal with dec_osf bug

Moving executable method to Wrapper base, removing global TMP variables where possible

Closing AlignIO to avoid too many open files error

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Alignment::DBA

Moving executable method to Wrapper base, removing global TMP variables where possible

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

To Quieten declaration warnings

Bio::Tools::Run::Alignment::Lagan

Poh. Lagan being a MSA program, it belongs into the Bio::Tools::Run::Alignment namespace

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Swapping order so that it won't fail on an isa of an array

Small fixes and addition of options

Really should include the program name

Bio::Tools::Run::Alignment::Sim4

Sim4 wrapper

Housekeeping for open files

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

To Quieten declaration warnings

Bio::Tools::Run::Alignment::StandAloneFasta

Committing first port of StandAloneFasta from Tiequan, may not be fully functional

Fix bug

Argh left out program_dir

Small fixes for linux and setting of program param correctly

Need to override executable to store multiple program namesTempfile cleanup may not be correct - need to verify

Support -S and a place to put the 'output' data - although not used yet

Bug which was not caught before

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Alignment::TCoffee

Use proper Tools::WrapperBase now

Codeml --> tcoffee copy+paste silliness

More robust parameter handling, matrix is not a required parameter (default of blosum), generic run method now

Make sure we've closed temporary file handles

Moving executable method to Wrapper base, removing global TMP variables where possible

Cleaned docs for cleanup()

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Analysis

Added a general Analysis client together with its incarnation as a SOAP client

Added -timeout parameter to the SOAP-based Analysis client

Bio::Tools::Run::Analysis::soap

Added a general Analysis client together with its incarnation as a SOAP client

Added -timeout parameter to the SOAP-based Analysis client

Changes in Soaplab API

Changes in Soaplab API

Bio::Tools::Run::AnalysisFactory

Added a general Analysis client together with its incarnation as a SOAP client

Added -timeout parameter to the SOAP-based Analysis client

Bio::Tools::Run::AnalysisFactory::Pise

Bioperl Pise: moving Bio::Factory::Pise to bioperl-run

Email not mandatory anymore in Pise

Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT and SEE ALSO parts.

- Piseapplication.pm, AnalysisFactory/Pise.pm and PiseJob.pm: -remote parameter to -location to conform to Bio::Tools::Run::AnalysisFactory interface - PiseApplication/genscan.pm: The documentation of all PiseApplication/*.pm files is going to change: in addition to COPYRIGHT, FEEDBACK SEE ALSO section, the DESCRIPTION section now contains *only* the parameters that can be set by the client. "Fake" parameters such as "Results" or "Paragraph" are no longer displayed here. => I commit only genscan.pm to let bioperl core see if it's ok :-)

Bio::Tools::Run::AnalysisFactory::soap

Added a general Analysis client together with its incarnation as a SOAP client

Changes in Soaplab API

Bio::Tools::Run::Blat

Wrapper for blat...still under dev

Wrapper for Blat

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Changes in align subroutine taking only one argument

Moving to Bio::Tools::Run::Alignment Namespace

Bio::Tools::Run::Coil

Wrapper for coil

Added quiet param, moving executable method to base class

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::EMBOSSApplication

No more warnings under perl 5.8.0

Added a missing semicolon to make the synopsis runnable

Use debug to print out the dumper info

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::EMBOSSacd

No more warnings under perl 5.8.0

Bio::Tools::Run::Eponine

Fixed Eponine test and runnable

Trying to add sanity to bioperl-run, added checks and pretty failures in the tests... will get there one day

Make sure resources are freed

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

More standardized way of running Eponine

Bio::Tools::Run::FootPrinter

First wrapper for Blanchette's FootPrinter for Phylogenetic Footprinting Todo, take in Bio::Tree for tree_of_life Smarter handling of seq ids

Close file handles

Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)

Moving executable method to Wrapper base, removing global TMP variables where possible

Cleaned docs for cleanup()

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Write the files properly

Bio::Tools::Run::Genewise

First addition of Genewise wrapper module

Few small fixes to Genewise runnable and test

Uses the parser in Bio::Tools::Genscan instead of internal parsing

Refactor wrapper

Added -trev option

Remove Fugu system stuff and insure that File tmp handles are closed -- this is what creates the problems of running out of filehandles

Make sure resources are freed

Support -u and -v settings, support passing in file instead of Bio::Seq object (trust user to do the right thing here and passing fastafile

Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)

Support HMMER filetype parameter

Oops - meant to set the HMMER param in the right place, also support another set of GENEWISE parameters

Let's create one less temporary file -- also - let's use the filehandle that was created for us, one less open call, support quiet operation

Quiet properly

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.

Clarified HMM support. Added checks & exception. Added docs

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Added more options

Bio::Tools::Run::Genscan

Allow suppression of stderr

Make sure resources are freed

Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Doc fix

Bio::Tools::Run::Hmmpfam

Wrapper module for hmmpfam

Check for options

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Updated to set params properly and return searchio object

Bio::Tools::Run::Lagan

Moved from bioperl-live. Note: name change: Bio::Tools::Lagan -> Bio::Tools::Run::Lagan

Poh. Lagan being a MSA program, it belongs into the Bio::Tools::Run::Alignment namespace

Bio::Tools::Run::Phylo::Molphy::ProtML

Synopsis doc

Moving executable method to Wrapper base, removing global TMP variables where possible

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Phylo::PAML::Codeml

Handle exe apps

Default should be F3X4

Respect the original cwd

Refer to the correct base class

Moving executable method to Wrapper base, removing global TMP variables where possible

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Phylo::PAML::Yn00

Fixed to work with new base object and use bioperl PAML parser

Add some debugging support

Moving executable method to Wrapper base, removing global TMP variables where possible

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Phylo::Phylip::Base

Should read correct filename for output, and allows one to programatically set the output and treefiles for phylip apps

Tree drawing modules

Use tempdir to run things

First stab at configuration files for managing version difference of phylip

Moving executable method to Wrapper base, removing global TMP variables where possible

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Phylo::Phylip::Consense

Wrapper for consense

Allow outgroups to be set using names

Changes to allow multiple alignments, matrices

Moving executable method to Wrapper base, removing global TMP variables where possible

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Phylo::Phylip::DrawGram

Tree drawing modules

Use tempdir to run things

Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming to run method

Don't need to cat tempdir if its an absolute path

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Phylo::Phylip::DrawTree

Tree drawing modules

Use tempdir to run things

Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming to run method

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Phylo::Phylip::Neighbor

Skip if ret val is 0

Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)

Should read correct filename for output, and allows one to programatically set the output and treefiles for phylip apps

Tree drawing modules

Use tempdir to run things

Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly

First stab at configuration files for managing version difference of phylip

Allow outgroups to be set using names

Changes to allow multiple alignments, matrices

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming to run method

Require jumble parameter to be odd or we get ina bad infinite loop

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Check for multiple data sets and set parameter accordingly. Caught by Vladimir.

Bio::Tools::Run::Phylo::Phylip::PhylipConf

First stab at configuration files for managing version difference of phylip

Added seqboot

Added consense

Changes to allow multiple alignments, matrices

JIT should be JTT

Bio::Tools::Run::Phylo::Phylip::ProtDist

Consistency

Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)

Small formatting changes

Should read correct filename for output, and allows one to programatically set the output and treefiles for phylip apps

Tree drawing modules

Use tempdir to run things

Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly

First stab at configuration files for managing version difference of phylip

Changes to allow multiple alignments, matrices

Moving executable method to Wrapper base, removing global TMP variables where possible

Formatting

Renaming to run method

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Phylo::Phylip::ProtPars

Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)

Tree drawing modules

Use the new Phylip base wrapper

Doc + code formatting cleanup

Use tempdir to run things

Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly

First stab at configuration files for managing version difference of phylip

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming to run method

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Phylo::Phylip::SeqBoot

Seqboot wrapper, only working with v3.5 currently

Changes to allow multiple alignments, matrices

Moving executable method to Wrapper base, removing global TMP variables where possible

Handle interleaved output from phylip 3.6, handle 3.6 in general

Remove debugging code

Allow more than one alignment

Bio::Tools::Run::PiseApplication

Bioperl Pise: moving Bio::Factory::Pise to bioperl-run

Email not mandatory anymore in Pise

Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT and SEE ALSO parts.

- Piseapplication.pm, AnalysisFactory/Pise.pm and PiseJob.pm: -remote parameter to -location to conform to Bio::Tools::Run::AnalysisFactory interface - PiseApplication/genscan.pm: The documentation of all PiseApplication/*.pm files is going to change: in addition to COPYRIGHT, FEEDBACK SEE ALSO section, the DESCRIPTION section now contains *only* the parameters that can be set by the client. "Fake" parameters such as "Results" or "Paragraph" are no longer displayed here. => I commit only genscan.pm to let bioperl core see if it's ok :-)

Bio::Tools::Run::PiseApplication::Puzzle

Puzzle interface update : - Add missing amino-acid substitution models. - Alignment file is now set on the command line.

Bio::Tools::Run::PiseApplication::clustalw_convert

Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).

Bio::Tools::Run::PiseApplication::dialign2

Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).

Bio::Tools::Run::PiseApplication::genscan

- Piseapplication.pm, AnalysisFactory/Pise.pm and PiseJob.pm: -remote parameter to -location to conform to Bio::Tools::Run::AnalysisFactory interface - PiseApplication/genscan.pm: The documentation of all PiseApplication/*.pm files is going to change: in addition to COPYRIGHT, FEEDBACK SEE ALSO section, the DESCRIPTION section now contains *only* the parameters that can be set by the client. "Fake" parameters such as "Results" or "Paragraph" are no longer displayed here. => I commit only genscan.pm to let bioperl core see if it's ok :-)

Bio::Tools::Run::PiseApplication::grailclnt

Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).

Bio::Tools::Run::PiseApplication::neighbor

Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).

Bio::Tools::Run::PiseApplication::pdbsearch

Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).

Bio::Tools::Run::PiseApplication::prot_nucml

Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).

Bio::Tools::Run::PiseApplication::quicktree

Pise: added quicktree, bug fix in PiseJob.pm

Bio::Tools::Run::PiseApplication::toppred

Bioperl Pise: moving Bio::Factory::Pise to bioperl-run

Bio::Tools::Run::PiseJob

Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).

Clean up to make -w clean

User agent version and job stdout/stderr mtd name

Pise: added quicktree, bug fix in PiseJob.pm

Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT and SEE ALSO parts.

- Piseapplication.pm, AnalysisFactory/Pise.pm and PiseJob.pm: -remote parameter to -location to conform to Bio::Tools::Run::AnalysisFactory interface - PiseApplication/genscan.pm: The documentation of all PiseApplication/*.pm files is going to change: in addition to COPYRIGHT, FEEDBACK SEE ALSO section, the DESCRIPTION section now contains *only* the parameters that can be set by the client. "Fake" parameters such as "Results" or "Paragraph" are no longer displayed here. => I commit only genscan.pm to let bioperl core see if it's ok :-)

Bio::Tools::Run::PiseJobParser

Pise: added warning handling in parser

Clean up to make -w clean

Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT and SEE ALSO parts.

Bio::Tools::Run::Primate

Make sure resources are freed

Changed to seqname to seq_id

Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Prints

Make sure resources are freed

Executable name change

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Profile

Wrapper module for Profile

Make sure resources are freed

Name of program is pfscan

Add an Id header

Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Use seq_id

Bio::Tools::Run::Promoterwise

Initial check in for promoterwise

Group hsps together as subseqfeatures

Using parser

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Pseudowise

Make sure resources are freed

Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)

Changed the parser to store the ka/ks ratio

Make quieten test work

Remove Kiran's hardcoded path to exe

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::RemoteBlast

Matthew's Changes committed: Add support to save_output. Add fix to put fasta header into QUERY line so query output has Query name. Add support to accept PROGRAM, DATABASE, EXPECT vars like MATRIX_NAME, etc.

Fix synopsis example for save_output, doesn't take rid.

Update SYNOPSIS code so that it runs

Change QUERY to use sequence display_id rather than primary_id

Remove commented lines, minor cleanup of header

Free resources

Moving remote blast into core

Bio::Tools::Run::RepeatMasker

Tiny extra curly brace

Moving parsing code out of wrapper

Make sure resources are freed

Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)

Move quiet to a wrapper param

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.

Cleaned docs for cleanup()

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Seg

Wrapper module for seg program

Wrapper module for Seg(Documentation changes)

Make sure resources are freed

Can run tests if we let executeable find the exe

Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::Signalp

wrapper for signalp

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::StandAloneBlast

Convert StandAloneBlast to WrapperBase (finallyperl -I. -w t/StandAloneBlast.t) -- need to test in different environments now

Fixed Issue #1354 from bugzilla, improved test to report more error details

This is really what I meant by splitting up these conditionals - careful about blindly committing submitted patches

Made docs slightly more clear (still long ways to go IMHO)

Deal with changes needed as seen by Issue #1359, mostly this is just a needed map_chars call in StandAloneBlast but have cleaned up the code some in other places

Moving standaloneblast from bioperl-run

Bio::Tools::Run::Tmhmm

Wrapper module for Tmhmm(Documentation changes)

Insure filehandles are closed

Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)

Moving executable method to Wrapper base, removing global TMP variables where possible

Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.

Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen

Bio::Tools::Run::TribeMCL

Added consensus description generation, with dependency on Algorith::Diff

Brought up to spec with the new Objects and seqname --> seq_id transition Don't use my %hash = undef; we get warnings, initialize to () Also insuring that tmp filehandles are closed to insure freeing of resources

Forgot to commit

Separated parameters for tribe-matrix and mcl in MATRIXPROGRAM_PARAMS and MCLPROGRAM_PARAMS. To discriminate upper and lower case parameters, in particular for mcl, AUTOLOAD is case sensitive when for unallowed parameters. Changed as consequences the way to build the command line in _run_matrix and _run_mcl methods. in _consensifier make sure that UNKNOWN has confidence_annotation_score equal to 0.

Checks to quieten tests

Do require for Algorithm::Diff

Moving executable method to Wrapper base, removing global TMP variables where possible

Bio::Tools::Run::Vista

Vista wrapper taking in SimpleAlign object and generate pdfs

Support more options

Bug, don't reverse seq

More docs

Makefile.PL

Skipping Pise tests if XML::Parser::SAX not installed, added dependency in Makefile

SAX/Sax -> PerlSAX

Added dependency to HTML::PArser which caused Pise tests to fail if not present

Added Algorithm::Diff dependency for TribeMCL

examples/pise/blast2.pl

Bioperl Pise: moving Bio::Factory::Pise to bioperl-run

Pise: added data for examples

examples/pise/clustalw.pl

Bioperl Pise: moving Bio::Factory::Pise to bioperl-run

examples/pise/dnadist.data

Pise: added data for examples

examples/pise/dnadist.pl

Bioperl Pise: moving Bio::Factory::Pise to bioperl-run

Pise: added data for examples

examples/pise/genscan.pl

Bioperl Pise: moving Bio::Factory::Pise to bioperl-run

Pise: added data for examples

examples/pise/needle.pl

Bioperl Pise: moving Bio::Factory::Pise to bioperl-run

examples/pise/toppred.pl

Bioperl Pise: moving Bio::Factory::Pise to bioperl-run

scripts/panalysis.PLS

Added a general Analysis client together with its incarnation as a SOAP client

Added -timeout parameter to the SOAP-based Analysis client

Changes in Soaplab API

scripts/papplmaker.PLS

Added a general Analysis client together with its incarnation as a SOAP client

Changes in Soaplab API

scripts/run_neighbor.PLS

Some scripts for running protdist and neighbor, for easy use in the bsub world

scripts/run_protdist.PLS

Some scripts for running protdist and neighbor, for easy use in the bsub world