/******************************COPYRIGHT NOTICE*******************************/ /* (c) Centro de Regulacio Genomica */ /* and */ /* Cedric Notredame */ /* 12 Aug 2014 - 22:07. */ /*All rights reserved. */ /*This file is part of T-COFFEE. */ /* */ /* T-COFFEE is free software; you can redistribute it and/or modify */ /* it under the terms of the GNU General Public License as published by */ /* the Free Software Foundation; either version 2 of the License, or */ /* (at your option) any later version. */ /* */ /* T-COFFEE is distributed in the hope that it will be useful, */ /* but WITHOUT ANY WARRANTY; without even the implied warranty of */ /* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the */ /* GNU General Public License for more details. */ /* */ /* You should have received a copy of the GNU General Public License */ /* along with Foobar; if not, write to the Free Software */ /* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */ /*............................................... */ /* If you need some more information */ /* cedric.notredame@europe.com */ /*............................................... */ /******************************COPYRIGHT NOTICE*******************************/ /* PROGRAM PATH - DO NOT CHANGE MANUALLY THIS FILE -- It is generated automatically by the build process -- See the 'update' target in the 'makefile' for more details */ //ERROR MESSAGES #define ADDRESS_BUILT_IN "built_in" #define PROGRAM_BUILT_IN "t_coffee" #define TEST_WWWSITE_4_TCOFFEE "www.google.com" //TclinkdbStart /********************************************/ /* Predictions */ /********************************************/ #define RNAPLFOLD_4_TCOFFEE "RNAplfold" #define RNAPLFOLD_ADDRESS "http://www.tbi.univie.ac.at/~ivo/RNA/" #define HMMTOP_4_TCOFFEE "hmmtop" #define HMMTOP_ADDRESS "www.enzim.hu/hmmtop/" #define GOR4_4_TCOFFEE "gorIV" #define GOR4_ADDRESS "http://mig.jouy.inra.fr/logiciels/gorIV/" /********************************************/ /* SEQUENCE ALIGNMENT */ /********************************************/ /*MSA Methods*/ #define CLUSTALW_4_TCOFFEE "clustalw" #define CLUSTALW_ADDRESS "ftp://www.ebi.ac.uk/pub/clustalw" #define CLUSTALW2_4_TCOFFEE "clustalw2" #define CLUSTALW2_ADDRESS "http://www.clustal.org" #define CLUSTALO_ADDRESS "http://www.clustal.org/omega/" #define CLUSTALO_4_TCOFFEE "clustalo" #define POA_4_TCOFFEE "poa" #define POA_ADDRESS "http://www.bioinformatics.ucla.edu/poa/" #define POA_DIR "/usr/share/" #define POA_FILE1 "blosum80.mat" #define PROBCONS_4_TCOFFEE "probcons" #define PROBCONSRNA_4_TCOFFEE "probconsRNA" #define PROBCONS_ADDRESS "http://probcons.stanford.edu/" #define DIALIGNT_4_TCOFFEE "dialign-t" #define DIALIGNT_ADDRESS "http://dialign-t.gobics.de/" #define DIALIGNT_DIR "/usr/share/dialign-t/" #define DIALIGNTX_4_TCOFFEE "dialign-tx" #define DIALIGNTX_ADDRESS "http://dialign-tx.gobics.de/" #define DIALIGNTX_DIR "/usr/share/dialign-tx/" #define MAFFT_4_TCOFFEE "mafft" #define MAFFT_ADDRESS "http://align.bmr.kyushu-u.ac.jp/mafft/online/server/" #define MUSCLE_4_TCOFFEE "muscle" #define MUSCLE_ADDRESS "http://www.drive5.com/muscle/" #define TCOFFEE_4_TCOFFEE "t_coffee" #define TCOFFEE_ADDRESS "http://www.tcoffee.org" #define PCMA_4_TCOFFEE "pcma" #define PCMA_ADDRESS "ftp://iole.swmed.edu/pub/PCMA/" #define KALIGN_4_TCOFFEE "kalign" #define KALIGN_ADDRESS "http://msa.cgb.ki.se" #define AMAP_4_TCOFFEE "amap" #define AMAP_ADDRESS "http://bio.math.berkeley.edu/amap/" #define PRODA_4_TCOFFEE "proda" #define PRODA_ADDRESS "http://proda.stanford.edu/" #define PRANK_4_TCOFFEE "prank" #define PRANK_ADDRESS "http://www.ebi.ac.uk/goldman-srv/prank/" #define CONSAN_4_TCOFFEE "sfold" #define CONSAN_ADDRESS "http://selab.janelia.org/software/consan/" /********************************************/ /* BLAST CLIEENTS */ /********************************************/ #define EBIWUBLASTc_4_TCOFFEE "wublast.pl" #define EBIWUBLASTc_ADDRESS "built_in" //#define EBIWUBLASTc_ADDRESS "http://www.ebi.ac.uk/Tools/webservices/services/wublast" #define EBIBLASTPGPc_4_TCOFFEE "blastpgp.pl" #define EBIBLASTPGPc_ADDRESS "built_in" #define NCBIBLAST_4_TCOFFEE "legacy_blast.pl" #define NCBIBLAST_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST" //coffee_pot_dbEnd /*Blast Server*/ /* BLAST_4_TCOFFEE can take the following values: NCBI ->use blastcl3 ftp://ftp.ncbi.nih.gov/blast/network/netblast/ SIB ->contact the sib LOCAL ->you must have blast installed */ /********************************************/ /* STRUCTURE ALIGNMENT */ /********************************************/ #define DALILITEc_4_TCOFFEE "dalilite.pl" #define DALILITEc_ADDRESS "built_in" /*Sap*/ #define SAP_4_TCOFFEE "sap" #define SAP_ADDRESS "http://mathbio.nimr.mrc.ac.uk/wiki/Software" /*TM-Align*/ #define TMALIGN_4_TCOFFEE "TMalign" #define TMALIGN_ADDRESS "http://zhang.bioinformatics.ku.edu/TM-align/" /*Mustang*/ #define MUSTANG_4_TCOFFEE "mustang" #define MUSTANG_ADDRESS "http://www.cs.mu.oz.au/~arun/mustang/" #define LSQMAN_4_TCOFFEE "lsqman" /*Align_pdb*/ #define ALIGN_PDB_4_TCOFFEE "align_pdb" /*Fugue*/ #define FUGUE_4_TCOFFEE "fugueali" #define FUGUE_ADDRESS "http://www-cryst.bioc.cam.ac.uk/fugue/download.html" //TclinkdbEnd /*New Methods*/ /********************************************/ /* Various Methoids */ /********************************************/ #define METHODS_4_TCOFFEE "~/.t_coffee/methods/" #define METHOD_4_MSA_WEIGHTS "petra_weight" /********************************************/ /* SEQAN LIBRARY */ /********************************************/ #define SEQAN_TCOFFEE_4_TCOFFEE "seqan_tcoffee" /********************************************/ /* REFORMATING AND UTILITIES */ /********************************************/ #define WGET_4_TCOFFEE "wget" #define WGET_ADDRESS "http://www.gnu.org/software/wget/" #define CURL_4_TCOFFEE "curl" #define CURL_ADDRESS "http://curl.haxx.se/" #define SEQ_REFORMAT_4_TCOFFEE "seq_reformat" #define PS2PDF "ps2pdf" #define EXTRACT_FROM_PDB_4_TCOFFEE "extract_from_pdb" #define BLAST_ALN2FASTA_ALN "blast_aln2fasta_aln.pl" #define FASTA_ALN2FASTA_ALN_UNIQUE_NAME "fasta_aln2fasta_aln_unique_name.pl" #define MSF_ALN2FASTA_ALN "msf_aln2fasta_aln.pl" #define SEQ2MSA_WEIGHT "seq2msa_weight" /********************************************/ /* DEPRECATED DEF */ /********************************************/ //Deprecated definitions #define SIB_BLAST_4_TCOFFEE "blastall.remote" #define LOCAL_BLAST_4_TCOFFEE "blastall" #define BLAST_DB_4_TCOFFEE "nr" #define NCBI_BLAST_4_TCOFFEE "" /********************************************/ /* PARAMETER_FILE */ /********************************************/ /* PARAMETER FILES */ #define COLOR_FILE "seq_reformat.color" /*This file specifies the 10 colors available to seq_reformat. If the file is not on the system, hard coded defaults will be used. The format is as follow: ------------------------------------------------------------------------------------------- * ------------------------------------------------------------------------------------------- the RGB values are used for the post-script generation, the html code is used in html documents. */