/******************************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 #define TCOFFEE_4_TCOFFEE "t_coffee" #define TCOFFEE_type "sequence_multiple_aligner" #define TCOFFEE_ADDRESS "http://www.tcoffee.org" #define TCOFFEE_language "C++" #define TCOFFEE_language2 "CXX" #define TCOFFEE_source "http://www.tcoffee.org/Packages/T-COFFEE_distribution.tar.gz" #define TCOFFEE_update_action "always" #define TCOFFEE_mode "tcoffee,mcoffee,rcoffee,expresso,3dcoffee" #define CLUSTALO_4_TCOFFEE "clustalo" #define CLUSTALO_type "sequence_multiple_aligner" #define CLUSTALO_ADDRESS "http://www.clustal.org/omega/" #define CLUSTALO_language "C++" #define CLUSTALO_language2 "C++" #define CLUSTALO_source "http://www.clustal.org/omega/clustal-omega-1.1.0.tar.gz" #define CLUSTALO_mode "mcoffee" #define CLUSTALO_version "1.1.0" #define STRIKE_4_TCOFFEE "strike" #define STRIKE_type "sequence_alignment_scoring" #define STRIKE_ADDRESS "http://www.tcoffee.org/Projects/strike/index.html" #define STRIKE_language "C++" #define STRIKE_language2 "CXX" #define STRIKE_source "http://www.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2" #define STRIKE_mode "tcoffee,expresso" #define STRIKE_version "1.2" #define CLUSTALW2_4_TCOFFEE "clustalw2" #define CLUSTALW2_type "sequence_multiple_aligner" #define CLUSTALW2_ADDRESS "http://www.clustal.org" #define CLUSTALW2_language "C++" #define CLUSTALW2_language2 "CXX" #define CLUSTALW2_source "http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz" #define CLUSTALW2_mode "mcoffee,rcoffee" #define CLUSTALW2_version "2.0.10" #define CLUSTALW_4_TCOFFEE "clustalw" #define CLUSTALW_type "sequence_multiple_aligner" #define CLUSTALW_ADDRESS "http://www.clustal.org" #define CLUSTALW_language "C" #define CLUSTALW_language2 "C" #define CLUSTALW_source "http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1.82.UNIX.tar.gz" #define CLUSTALW_mode "mcoffee,rcoffee" #define CLUSTALW_version "1.82" #define DIALIGNT_4_TCOFFEE "dialign-t" #define DIALIGNT_type "sequence_multiple_aligner" #define DIALIGNT_ADDRESS "http://dialign-tx.gobics.de/" #define DIALIGNT_DIR "/usr/share/dialign-tx/" #define DIALIGNT_language "C" #define DIALIGNT_language2 "C" #define DIALIGNT_source "http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz" #define DIALIGNT_mode "mcoffee" #define DIALIGNT_binary "dialign-t" #define DIALIGNT_version "1.0.2" #define DIALIGNTX_4_TCOFFEE "dialign-tx" #define DIALIGNTX_type "sequence_multiple_aligner" #define DIALIGNTX_ADDRESS "http://dialign-tx.gobics.de/" #define DIALIGNTX_DIR "/usr/share/dialign-tx/" #define DIALIGNTX_language "C" #define DIALIGNTX_language2 "C" #define DIALIGNTX_source "http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz" #define DIALIGNTX_mode "mcoffee" #define DIALIGNTX_binary "dialign-tx" #define DIALIGNTX_version "1.0.2" #define POA_4_TCOFFEE "poa" #define POA_type "sequence_multiple_aligner" #define POA_ADDRESS "http://www.bioinformatics.ucla.edu/poa/" #define POA_language "C" #define POA_language2 "C" #define POA_source "http://downloads.sourceforge.net/poamsa/poaV2.tar.gz" #define POA_DIR "/usr/share/" #define POA_FILE1 "blosum80.mat" #define POA_mode "mcoffee" #define POA_binary "poa" #define POA_version "2.0" #define PROBCONS_4_TCOFFEE "probcons" #define PROBCONS_type "sequence_multiple_aligner" #define PROBCONS_ADDRESS "http://probcons.stanford.edu/" #define PROBCONS_language2 "CXX" #define PROBCONS_language "C++" #define PROBCONS_source "http://probcons.stanford.edu/probcons_v1_12.tar.gz" #define PROBCONS_mode "mcoffee" #define PROBCONS_binary "probcons" #define PROBCONS_version "1.12" #define MAFFT_4_TCOFFEE "mafft" #define MAFFT_type "sequence_multiple_aligner" #define MAFFT_ADDRESS "http://align.bmr.kyushu-u.ac.jp/mafft/online/server/" #define MAFFT_language "C" #define MAFFT_language "C" #define MAFFT_source "http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-with-extensions-src.tgz" #define MAFFT_windows "http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-mingw.tar" #define MAFFT_mode "mcoffee,rcoffee" #define MAFFT_binary "mafft.tar.gz" #define MAFFT_version "6.603" #define MUSCLE_4_TCOFFEE "muscle" #define MUSCLE_type "sequence_multiple_aligner" #define MUSCLE_ADDRESS "http://www.drive5.com/muscle/" #define MUSCLE_language "C++" #define MUSCLE_language2 "GPP" #define MUSCLE_source "http://www.drive5.com/muscle/downloads3.7/muscle3.7_src.tar.gz" #define MUSCLE_windows "http://www.drive5.com/muscle/downloads3.7/muscle3.7_win32.zip" #define MUSCLE_linux "http://www.drive5.com/muscle/downloads3.7/muscle3.7_linux_ia32.tar.gz" #define MUSCLE_mode "mcoffee,rcoffee" #define MUSCLE_version "3.7" #define MUS4_4_TCOFFEE "mus4" #define MUS4_type "sequence_multiple_aligner" #define MUS4_ADDRESS "http://www.drive5.com/muscle/" #define MUS4_language "C++" #define MUS4_language2 "GPP" #define MUS4_source "http://www.drive5.com/muscle/muscle4.0_src.tar.gz" #define MUS4_mode "mcoffee,rcoffee" #define MUS4_version "4.0" #define PCMA_4_TCOFFEE "pcma" #define PCMA_type "sequence_multiple_aligner" #define PCMA_ADDRESS "ftp://iole.swmed.edu/pub/PCMA/" #define PCMA_language "C" #define PCMA_language2 "C" #define PCMA_source "ftp://iole.swmed.edu/pub/PCMA/pcma.tar.gz" #define PCMA_mode "mcoffee" #define PCMA_version "1.0" #define KALIGN_4_TCOFFEE "kalign" #define KALIGN_type "sequence_multiple_aligner" #define KALIGN_ADDRESS "http://msa.cgb.ki.se" #define KALIGN_language "C" #define KALIGN_language2 "C" #define KALIGN_source "http://msa.cgb.ki.se/downloads/kalign/current.tar.gz" #define KALIGN_mode "mcoffee" #define KALIGN_version "1.0" #define AMAP_4_TCOFFEE "amap" #define AMAP_type "sequence_multiple_aligner" #define AMAP_ADDRESS "http://bio.math.berkeley.edu/amap/" #define AMAP_language "C++" #define AMAP_language2 "CXX" #define AMAP_source "http://amap-align.googlecode.com/files/amap.2.0.tar.gz" #define AMAP_mode "mcoffee" #define AMAP_version "2.0" #define PRODA_4_TCOFFEE "proda" #define PRODA_type "sequence_multiple_aligner" #define PRODA_ADDRESS "http://proda.stanford.edu" #define PRODA_language "C++" #define PRODA_language2 "CXX" #define PRODA_source "http://proda.stanford.edu/proda_1_0.tar.gz" #define PRODA_mode "mcoffee" #define PRODA_version "1.0" #define FSA_4_TCOFFEE "fsa" #define FSA_type "sequence_multiple_aligner" #define FSA_ADDRESS "http://fsa.sourceforge.net/" #define FSA_language "C++" #define FSA_language2 "CXX" #define FSA_source "http://sourceforge.net/projects/fsa/files/fsa-1.15.3.tar.gz/download/" #define FSA_mode "mcoffee" #define FSA_version "1.15.3" #define PRANK_4_TCOFFEE "prank" #define PRANK_type "sequence_multiple_aligner" #define PRANK_ADDRESS "http://www.ebi.ac.uk/goldman-srv/prank/" #define PRANK_language "C++" #define PRANK_language2 "CXX" #define PRANK_source "http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.100802.tgz" #define PRANK_mode "mcoffee" #define PRANK_version "100303" #define SAP_4_TCOFFEE "sap" #define SAP_type "structure_pairwise_aligner" #define SAP_ADDRESS "http://mathbio.nimr.mrc.ac.uk/wiki/Software" #define SAP_language "C" #define SAP_language2 "C" #define SAP_source "http://mathbio.nimr.mrc.ac.uk/download/SAP/sap-1.1.3.tar.gz" #define SAP_mode "expresso,3dcoffee" #define SAP_version "1.1.3" #define TMALIGN_4_TCOFFEE "TMalign" #define TMALIGN_type "structure_pairwise_aligner" #define TMALIGN_ADDRESS "http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.f" #define TMALIGN_language "Fortran" #define TMALIGN_language2 "Fortran" #define TMALIGN_source "http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.f" #define TMALIGN_linux "http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign_32.gz" #define TMALIGN_mode "expresso,3dcoffee" #define TMALIGN_version "2013.05.11" #define MUSTANG_4_TCOFFEE "mustang" #define MUSTANG_type "structure_pairwise_aligner" #define MUSTANG_ADDRESS "http://www.cs.mu.oz.au/~arun/mustang" #define MUSTANG_language "C++" #define MUSTANG_language2 "CXX" #define MUSTANG_source "http://ww2.cs.mu.oz.au/~arun/mustang/mustang_v3.2.1.tgz" #define MUSTANG_mode "expresso,3dcoffee" #define MUSTANG_version "3.2.1" #define LSQMAN_4_TCOFFEE "lsqman" #define LSQMAN_type "structure_pairwise_aligner" #define LSQMAN_ADDRESS "empty" #define LSQMAN_language "empty" #define LSQMAN_language2 "empty" #define LSQMAN_source "empty" #define LSQMAN_update_action "never" #define LSQMAN_mode "expresso,3dcoffee" #define ALIGN_PDB_4_TCOFFEE "align_pdb" #define ALIGN_PDB_type "structure_pairwise_aligner" #define ALIGN_PDB_ADDRESS "empty" #define ALIGN_PDB_language "empty" #define ALIGN_PDB_language2 "empty" #define ALIGN_PDB_source "empty" #define ALIGN_PDB_update_action "never" #define ALIGN_PDB_mode "expresso,3dcoffee" #define FUGUE_4_TCOFFEE "fugueali" #define FUGUE_type "structure_pairwise_aligner" #define FUGUE_ADDRESS "http://www-cryst.bioc.cam.ac.uk/fugue/download.html" #define FUGUE_language "empty" #define FUGUE_language2 "empty" #define FUGUE_source "empty" #define FUGUE_update_action "never" #define FUGUE_mode "expresso,3dcoffee" #define DALILITEc_4_TCOFFEE "dalilite.pl" #define DALILITEc_type "structure_pairwise_aligner" #define DALILITEc_ADDRESS "built_in" #define DALILITEc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/dalilite" #define DALILITEc_language "Perl" #define DALILITEc_language2 "Perl" #define DALILITEc_source "empty" #define DALILITEc_update_action "never" #define DALILITEc_mode "expresso,3dcoffee" #define PROBCONSRNA_4_TCOFFEE "probconsRNA" #define PROBCONSRNA_type "RNA_multiple_aligner" #define PROBCONSRNA_ADDRESS "http://probcons.stanford.edu/" #define PROBCONSRNA_language "C++" #define PROBCONSRNA_language2 "CXX" #define PROBCONSRNA_source "http://probcons.stanford.edu/probconsRNA.tar.gz" #define PROBCONSRNA_mode "mcoffee,rcoffee" #define PROBCONSRNA_version "1.0" #define CONSAN_4_TCOFFEE "sfold" #define CONSAN_type "RNA_pairwise_aligner" #define CONSAN_ADDRESS "http://selab.janelia.org/software/consan/" #define CONSAN_language "empty" #define CONSAN_language2 "empty" #define CONSAN_source "empty" #define CONSAN_update_action "never" #define CONSAN_mode "rcoffee" #define RNAPLFOLD_4_TCOFFEE "RNAplfold" #define RNAPLFOLD_type "RNA_secondarystructure_predictor" #define RNAPLFOLD_ADDRESS "http://www.tbi.univie.ac.at/~ivo/RNA/" #define RNAPLFOLD_language "C" #define RNAPLFOLD_language2 "C" #define RNAPLFOLD_source "http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.7.2.tar.gz" #define RNAPLFOLD_mode "rcoffee," #define RNAPLFOLD_version "1.7.2" #define PHYLIP_4_TCOFFEE "retree" #define PHYLIP_type "RNA_secondarystructure_predictor" #define PHYLIP_ADDRESS "http://evolution.gs.washington.edu/phylip/" #define PHYLIP_language "C" #define PHYLIP_language2 "C" #define PHYLIP_source "http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz" #define PHYLIP_mode "trmsd," #define PHYLIP_version "3.69" #define HMMTOP_4_TCOFFEE "hmmtop" #define HMMTOP_type "protein_secondarystructure_predictor" #define HMMTOP_ADDRESS "www.enzim.hu/hmmtop/" #define HMMTOP_language "C" #define HMMTOP_language2 "C" #define HMMTOP_source "empty" #define HMMTOP_binary "hmmtop" #define HMMTOP_update_action "never" #define HMMTOP_mode "tcoffee" #define HMMTOP_version "2.1" #define GOR4_4_TCOFFEE "gorIV" #define GOR4_type "protein_secondarystructure_predictor" #define GOR4_ADDRESS "http://mig.jouy.inra.fr/logiciels/gorIV/" #define GOR4_language "C" #define GOR4_language2 "C" #define GOR4_source "http://mig.jouy.inra.fr/logiciels/gorIV/GOR_IV.tar.gz" #define GOR4_update_action "never" #define GOR4_mode "tcoffee" #define EBIWUBLASTc_4_TCOFFEE "wublast.pl" #define EBIWUBLASTc_type "protein_homology_predictor" #define EBIWUBLASTc_ADDRESS "built_in" #define EBIWUBLASTc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/wublast" #define EBIWUBLASTc_language "Perl" #define EBIWUBLASTc_language2 "Perl" #define EBIWUBLASTc_source "empty" #define EBIWUBLASTc_update_action "never" #define EBIWUBLASTc_mode "psicoffee,expresso,accurate" #define EBIBLASTPGPc_4_TCOFFEE "blastpgp.pl" #define EBIBLASTPGPc_type "protein_homology_predictor" #define EBIBLASTPGPc_ADDRESS "built_in" #define EBIBLASTPGPc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/blastpgp" #define EBIBLASTPGPc_language "Perl" #define EBIBLASTPGPc_language2 "Perl" #define EBIBLASTPGPc_source "empty" #define EBIBLASTPGPc_update_action "never" #define EBIBLASTPGPc_mode "psicoffee,expresso,accurate" #define blastall_4_TCOFFEE "blastall" #define blastall_type "protein_homology_predictor" #define blastall_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST" #define blastall_language "C" #define blastall_language2 "C" #define blastall_source "empty" #define blastall_update_action "never" #define blastall_mode "psicoffee,expresso,3dcoffee" #define NCBIBLAST_4_TCOFFEE "legacy_blast.pl" #define NCBIBLAST_type "protein_homology_predictor" #define NCBIBLAST_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST" #define NCBIBLAST_language "C" #define NCBIBLAST_language2 "C" #define NCBIBLAST_source "empty" #define NCBIBLAST_update_action "never" #define NCBIBLAST_mode "psicoffee,expresso,3dcoffee" #define SOAPLITE_4_TCOFFEE "SOAP::Lite" #define SOAPLITE_type "library" #define SOAPLITE_ADDRESS "http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL" #define SOAPLITE_language "Perl" #define SOAPLITE_language2 "Perl" #define SOAPLITE_source "empty" #define _update_action "never" #define SOAPLITE_mode "none" #define XMLSIMPLE_4_TCOFFEE "XML::Simple" #define XMLSIMPLE_type "library" #define XMLSIMPLE_ADDRESS "http://search.cpan.org/~grantm/XML-Simple-2.18/lib/XML/Simple.pm" #define XMLSIMPLE_language "Perl" #define XMLSIMPLE_language2 "Perl" #define XMLSIMPLE_source "empty" #define XMLSIMPLE_mode "psicoffee,expresso,accurate" //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. */