Author: tille Date: 2013-02-14 08:57:52 +0000 (Thu, 14 Feb 2013) New Revision: 13004
Added: trunk/packages/meme/trunk/debian/bin_list.txt Log: Include the list of useful binaries given by upstream here in SVN to help packaging. Might be removed before final upload once the list is turned into packaging code. Added: trunk/packages/meme/trunk/debian/bin_list.txt =================================================================== --- trunk/packages/meme/trunk/debian/bin_list.txt (rev 0) +++ trunk/packages/meme/trunk/debian/bin_list.txt 2013-02-14 08:57:52 UTC (rev 13004) @@ -0,0 +1,110 @@ +# This list was given by upstream James Johnson <[email protected]> at +# https://lists.alioth.debian.org/pipermail/debian-med-packaging/2013-February/018656.html +# It should be helpful for packaging - thanks to James for this list + +alphtype Webserver determines if a alphabet string is DNA or PROTEIN, I will probably reimplement as part of a Perl module +ama Useful calculates average/maximum motif score for sequences, first step in gomo analysis +ama-qvalues Useful calculates q-values for ama output +ame Useful calculates motif enrichment in sequences +beadstring Obsolete Obsoleted by MCAST +beeml2meme Useful converts motifs to MEME format from BEEML format +cat_max Fossil ... +centrimo Useful calculates areas of localised motif enrichment +ceqlogo Rarely Useful generates a single motif logo, it's not very user friendly and mostly called through the c interface +changetoweb Fossil ... +chen2meme Useful converts motifs to MEME format from Chen format +clustalw2fasta Possibly Useful converts sequences in clustalw format to fasta format +clustalw2phylip Possibly Useful converts sequences in clustalw format to phylip format +clustalw-io Not Useful allows testing of the clustalw parser +compare_dates Fossil another script used by the "download" script +compute-prior-dist Possibly Useful computes the distribution of priors in a MEME PSP file +compute-uniform-priors Possibly Useful computes a uniform prior psp file equal to the mean of all input priors in another psp file (missing doc) +create-priors Useful allows running MEME in discriminative mode by creating a position specific prior file +download Fossil old code for downloading sequence databases +draw-mhmm Possibly Useful produces a graphvis representation of a MHMM model +dreme Useful Discover short DNA motifs +dust Useful filters low complexity regions from sequences +fasta-center Possibly Useful filters a set of sequences to only leave the central region +fasta-dinucleotide-shuffle Useful shuffles a sequence while maintaining di-nucleotide frequencies +fasta-dinucleotide-shuffle.py Python Library I'll get this moved into the libs directory like with the Perl modules. +fasta-fetch Possibly Useful Seems to use an index generated by fasta-make-index to fetch sequences out of a fasta file +fasta-get-markov Useful generates a Markov model of letter frequencies used as backgrounds by many MEME Suite programs +fasta-hamming-enrich Possibly Useful compute the Hamming distance from a word to each sequence in two sets, apply Fisher Exact test +fasta-hamming-enrich.py Python Library ... +fasta-io Not Useful just allows testing of the fasta file reading +fasta-make-index Possibly Useful makes an index of a fasta file +fasta-most Useful finds the length of sequence that occurs most, used by MEME-ChIP +fasta-shuffle-letters Possibly Useful shuffles letters of a sequence, though fasta-dinucleotide-shuffle is better +fasta-subsample Useful selects a subset of the sequences +fasta-unique-names Possibly Useful makes sequence names unique, replaces U+0001 with space +fimo Useful searches for motif sites +fisher_exact Possibly Useful computes the result of the Fisher Exact test with the given numbers +fitevd Possibly Useful fits an extreme value distribution to a set of score-length pairs. +gendb Possibly Useful generates a synthetic fasta database from a background model +get_db_csv Webserver queries an online sequence repository for its databases and creates a csv file for update_db to use +getsize Useful measures statistics about a fasta file +glam2 Useful Discover gapped motifs +glam2format Possibly Useful converts GLAM2 output to FASTA (with gaps) or MSF +glam2html Useful converts GLAM2 output to HTML, called by glam2 but not often by users +glam2mask Useful used with GLAM2 to mask out found motifs and find weaker ones +glam2psfm Useful convert GLAM2 output to a MEME motif +glam2scan Useful scans a sequence with a GLAM2 motif +glam2scan2html Useful converts GLAM2SCAN output to HTML, called by glam2scan but not often by users +gomo Useful finds enriched GO terms associated with high ranking genes +gomo_highlight Useful post processes gomo XML output to include further information which makes the HTML better +hart2meme-bkg Possibly Useful Convert a Hartemink background to a MEME background +hartemink2psp Possibly Useful Convert a Hartemink PSP file into a MEME PSP file +hypergeometric.py Python Library ... +iupac2meme Useful Make a MEME motif from a IUPAC string +jaspar2meme Useful Convert motifs from JASPAR to MEME format +llr Possibly Useful Compute the probability distribution for the log-likelihood ratio (LLR) of N letters. +mast Useful Find sequences which best match a group of motifs +mast2txt Useful Convert mast XML output to mast text output. Called by mast +mcast Useful Find matches to a motif hidden markov model +meme Useful Discover motifs, this script calls meme.bin handling the details of parallelization +meme2images Useful Create motif logos for all motifs in a MEME motif file +meme2meme Useful Combine multiple MEME motif files into 1 +meme.bin Useful Discover motifs, this is typically called by the meme script +meme-chip Useful Discover motifs, look for enriched motifs, calls MEME, DREME, CentriMo, TOMTOM, eventually FIMO and SpaMo +meme-get-motif Possibly Useful Extract motifs from a MEME text file. +meme-rename Possibly Useful Renames all the output HTML files from MEME-ChIP so they can be kept in one folder and emailed easily +meme-xml-html Possibly Useful Does an XML transformation to convert XML output to HTML output, not actually specific to MEME +metameme Fossil Used to handle web jobs for metameme +mhmm Obsolete Given MEME motif, write a motif-based HMM, obsoleted by MCAST +mhmm2html Obsolete Convert MHMM output to HTML, obsoleted by MCAST +mhmme Obsolete obsoleted by MCAST +mhmm-io Not Useful allows testing of reading/writing MHMM models +mhmms Obsolete obsoleted by MCAST +mhmmscan Obsolete obsoleted by MCAST +motiph Possibly Useful part of a publised paper so we want to keep it around +nmica2meme Useful converts motifs from NMICA format to MEME format +oldmeme2meme Fossil converts reallly really old MEME files into only really old MEME files... +plotgen Webserver used to generate usage plots from the logs +pmp_bf Possibly Useful calculates the statistical power of a phylogenetic motif model +priority2meme Useful converts motifs in priority format to MEME format +prior_utils.pl Perl library ... +psp-gen Useful calculates PSP files for MEME +purge Possibly Useful filters sequences to remove repeats +qvalue Possibly Useful computes q-values from a list of p-values +ramen Useful (bugs?) integration was never tested so it may have major bugs, does regression analysis of motif enrichment +ranksum_test Possibly Useful calculates the rank-sum test +read_fasta_file.pl Perl Library ... +readseq Useful converts sequence formats +reconcile-tree-alignment Possibly Useful identify the intersection of the sets of sequence IDs and leaf labels +reduce-alignment Possibly Useful Extract specified columns from a multiple alignment. +remove-alignment-gaps Possibly Useful Remove from an alignment all columns that correspond to a gap in a specified species. +rna2meme Useful convert an RNA sequence to it's binding motif in MEME format +scpd2meme Useful convert motifs in SCPD format to MEME format +sd Possibly Useful calcualtes mean and standard deviation of a list of numbers +sequence.py Python Library ... +shadow Not Useful related to the motiph program but never went anywhere, Perform phylogenetic shadowing +spamo Useful motif spacing enrichment analysis +taipale2meme Useful converts motifs from Taipale format to MEME format +tamo2meme Useful converts motifs from TAMO format to MEME format +tomtom Useful comparison of DNA motifs +transfac2meme Useful converts motifs from Transfac matrics to MEME format +tree Obsolete obsoleted by MCAST +uniprobe2meme Useful convert motifs from Uniprobe format to MEME format +update_db Webserver download sequences listed on the page get_db_list.cgi if there timestamp is newer +update_meme_tests Not Useful updates the MEME and MAST smoke tests (they must be run first), shouldn't be needed by end users +xsltproc_lite Rarely Useful used to generate the documentation from XML, the next version will not need it _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
