ChangeLog 2006-03-01 Nadya Williams nadya@sdsc.edu * website/html/meme-install.html: add MacOS X startup * etc/meme-darwin.in, StartupParameters.plist: create MacOS X startup 2006-02-16 Nadya Williams nadya@sdsc.edu * website/html/general-faq.html, mast-input.html, meme-input.html, help_alphabet.html, mast-intro.html, meme-intro.html, help_distribution.html, help_format.html, mast-output.html, motif-format.html, meme-download.html, papers.html, mast-databases.html, release_notes.html, mast-faq.html : new web insterface changes provided by C. Misleh * website/html/template-css.js, template-footer.js, template-header.js, style-default.css : added for the new web interface, provided by C. Misleh 2006-02-16 Nadya Williams nadya@sdsc.edu * configure.ac: rm check dependency on parallel condition when creating server executables. * website/html/meme-install.html: add explanation of --with-url flag * website/cgi-bin/meme.pl, mast.pl, process_request.pl: fix path ot images/ * etc/meme.linux.in: fix description syntax 2006-01-24 Nadya Williams nadya@sdsc.edu * src/include/meme-cs.h: rm OS-dependent declarations of accept(), bind(), connect(), socket(), listen(), htons(). They are defined in system header files. * read_seq_file.c: add '\r' character to look for when delimiting strings this is a fix for cygwin newline representation * scripts/makelogodds.txt: add -f flag to shell 2006-01-24 Nadya Williams nadya@sdsc.edu * scripts/meme_config.txt: export environ settings needed for starting meme/mast servers. Add variable $EXT to handle echo output * scripts/runcheck: source meme_config to set environment, make output table-like * scripts/runtests.txt: use EXT for echo output, change "info" from array to string to make it work on solaris, change output to be table-like 2006-01-21 Nadya Williams nadya@sdsc.edu * website/html/meme-download.html: substitute link to userguide.html with meme-install.html * website/html/userguide.html: rm, use more updated meme-install.html 2006-01-20 Tim Bailey t.bailey@imb.uq.edu.au * src/starts.c: rm obsolete argument sample_prob from call to subseq7() 2006-01-19 Nadya Williams nadya@sdsc.edu * website/html/meme-install.html: add patching info 2006-01-09 Tim Bailey t.bailey@imb.uq.edu.au * src/subseq7.c: rm obsolete argument sample_prob from subseq7() * src/oops.c: fixed bug in e_step * src/include/meme.h: rm obsolete argument sample_prob from subseq7() 2006-01-03 Tim Bailey t.bailey@imb.uq.edu.au * etc/meme-explanation.html, webiste/html/meme-output-example.html: fix documentation of PSSM and PSPM * scripts/mast-client.txt: fix bug caused by typo "MEME_BINbin" * website/cgi-bin/meme.pl: fix use of min() 2005-12-21 Nadya Williams nadya@sdsc.edu * website/html/Makefile.am: add meme-install.html 2005-12-16 Nadya Williams nadya@sdsc.edu * etc/meme.solaris.in: fix server startup * etc/meme.cygwin.in: rm unix-related funcitons. Need verification testing * etc/meme.darwin.in: add script, a place holder to make compilation complete * scripts/Makefile.am: reorganize separation of scripts on server and client. * website/html/release_notes.html: add mac support 2005-12-16 Tim Bailey t.bailey@imb.uq.edu.au * etc/meme.cygwin.in: add script, a place holder to make compilation complete * src/include/meme-cs.h: add cygwin support 2005-12-15 Tim Bailey t.bailey@imb.uq.edu.au * src/getsize.c: unless -nd given, duplicate sequences are flagged and not counted * website/cgi-bin/meme.pl: Don't allow more than $MAXSITES sequences in OOPS mode. Set maxsites to minimum of number of sequences and $MAXSITES in ZOOPS mode 2005-12-15 Nadya Williams nadya@sdsc.edu * etc/Makefile.am: always install meme.bin and mast.bin 2005-12-13 Nadya Williams nadya@sdsc.edu * etc/Makefile.am: Make creation of startup script conditional on platform used 2005-12-09 Tim Bailey t.bailey@imb.uq.edu.au * website/html/mast.in, website/html/mast-databases.html: add detailed instructions for downloading upstream databases, put "K12" after E. coli database name to make clear which strain it is. 2005-12-02 Tim Bailey t.bailey@imb.uq.edu.au * scripts/usage-reports: removed the "meta-meme" update because the server no longer is running. Metameme update should be replaced when meta-meme comes back on line. 2005-12-01 Tim Bailey t.bailey@imb.uq.edu.au * scripts/meme2html.pl: add new button to MEME DNA output to submit PSPM to * website/cgi-bin/process_request.pl: add handling of JASPAR searches 2005-10-28 Nadya Williams nadya@sdsc.edu * src/mast-server.c: fix typo in "/bin/rm". The typo introduced a bug of leaving mast motif files in the LOGS/. * scripts/meme_config.txt: change MEME_LOGS to be configurable, add MEME_DB. * scripts/Makefile.am: add use of MEME_LOGS and MEME_DB. 2005-10-25 Nadya Williams nadya@sdsc.edu * src/pssm-distr.c, include/pssm-distr.h src/display.c: use only C-style comments * NSTALL, Makefile.am, configure.ac, etc/Makefile.am, etc/meme.csh.in, etc/meme.sh.in, website/scripts/Globals.txt, website/scripts/Makefile.am: make LOGS/ configurable by user during "configure". Defaults to $prefix/LOGS. 2005-10-20 Tim Bailey t.bailey@imb.uq.edu.au * scr/Makefile.am, src/parallel/Makefile.am: add pssm-distr.c to meme/mast sources * scr/include/mast.h: include pssm-distr.h, rm definition of calc_cdf() * scr/include/pssm-distr.h: add file 2005-10-19 Nadya Williams nadya@sdsc.edu * configure.ac: update specific irix6 and remove lmpi for LIBS This fixes the checking for new irix OS, and rm -lmpi form a serial compilation * src/include/meme-cs.h: add MACOSX define to prevent confilict with system defined. 2005-10-18 Nadya Williams nadya@sdsc.edu * website/examples/sample-kabat.seq, website/examples/sample-motif.seq: rm control-M 2005-10-13 Nadya Williams nadya@sdsc.edu * etc/meme-explanation.html: move from website/html/ to allow html converison of output files without installting website. * website/Makefile.am: always install Globals.pm, need for perl scripts 2005-10-07 Nadya Williams nadya@sdsc.edu * scripts/runcheck: clean debugging output that caused problem on Solaris * scripts/start-meme.txt, scripts/start-mast.txt, scripts/meme_config.csh.txt, scripts/meme.txt, scripts/mast.txt: keep uniform name MEME_LOGS throughout scripts * scripts/memd.txt: add check for existence of LOGS/ for writing tmp files, add diagnostic output for the case when no servers found 2005-10-06 Nadya Williams nadya@sdsc.edu * m4/functions.m4 m4/headers.m4: add definitions for configure macros that are missing from autoconf v < 2.54 These files are automatically added by executing "bootstrap" when needed * src/include/logs.h: redefine cast in log_table and exp_table because some SUN compilers cant reduce expression inside #define 2005-10-05 Nadya Williams nadya@sdsc.edu * scripts/update_meme_tests, scripts/update_mast_databases.txt, scripts/update-plot-usage.txt, scripts/texit, scripts/sd, scripts/runtests.txt, scripts/roc.txt, scripts/plotgen, scripts/plot-usage, scripts/meme-client.txt, scripts/fasta-make-index.txt, scripts/download: use full path for "rm". Assume everybody has /bin/rm 2005-10-04 Nadya Williams nadya@sdsc.edu * scripts/runcheck: change array with awk parsing and initialize err. This allows sh to work on solaris. * scripts/make_logodds.txt: use full path for "rm". Assume everybody has /bin/rm 2005-10-02 Nadya Williams nadya@sdsc.edu * src/Makefile.am: make adding libadd conditional in include switches. Now shows only when needed. * website/cgi-bin/mast.pl, website/cgi-bin/process-request.pl, website/cgi-bin/meme.pl: move meme-client and mast-client names to Globals.pm 2005-09 Nadya Williams nadya@sdsc.edu * for verison 3.5.0 (and after) use GNU automake/autoconf tools to install. Restructure directory tree, create configure.am, and all Makefile.am files. For changes in 3.0.14 and prior see website/html/release_notes.html/