[med-svn] r13004 - trunk/packages/meme/trunk/debian
Andreas Tille
tille at alioth.debian.org
Thu Feb 14 08:57:53 UTC 2013
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 <j.johnson at imb.uq.edu.au> 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
More information about the debian-med-commit
mailing list