$version = "1.6.3, September 2023";
$mode = "coassembly";
$date = "Mon Feb  5 09:21:07 2024";

$installpath = "/mnt/hpc/home/zhanglj/miniconda3/envs/squeezeMeta/SqueezeMeta";
$userdir       = "/mnt/hpc/home/zhanglj/squeezemetatrans/hr_data";
#-- Project dir (calculated dinamically on execution, DO NOT MODIFY)
use File::Basename;
use Cwd 'abs_path';
$projectdir   = abs_path(dirname(__FILE__));
#-- Generic paths
#$databasepath = "/media/disk7/fer/SqueezeMeta/db";
$databasepath = "/mnt/hpc/home/zhanglj/squeezeMeta/SqueezeMeta/database/db";
$extdatapath  = "$installpath/data";
$scriptdir    = "$installpath/scripts";   #-- Scripts directory
#-- Paths relative to the project
$projectname = "shotguntrans";
$datapath    = "$projectdir/data";                                       #-- Directory containing all datafiles
$resultpath  = "$projectdir/results";                                    #-- Directory for storing results
$extpath     = "$projectdir/ext_tables";                                 #-- Directory for storing tables for further analysis
$tempdir     = "$projectdir/temp";                                       #-- Temp directory
$interdir    = "$projectdir/intermediate";                               #-- Temp directory
$binresultsdir = "$resultpath/bins";						   #-- Directory for bins
%dasdir      = ("DASTool","$resultpath/DAS/$projectname\_DASTool\_bins");	   #-- Directory for DASTool results
#-- Customizable binning and assembly
%assemblers  = ("megahit","assembly_megahit.pl","spades","assembly_spades.pl","rnaspades", "assembly_rnaspades.pl", "spades-base", "assembly_spades-base.pl", "canu","assembly_canu.pl","flye","assembly_flye.pl");
%binscripts  = ("maxbin","$installpath/lib/SqueezeMeta/bin_maxbin.pl","metabat2","$installpath/lib/SqueezeMeta/bin_metabat2.pl","concoct","$installpath/lib/SqueezeMeta/bin_concoct.pl");
#-- Result files
$mappingfile     = "$datapath/00.$projectname.samples";         #-- Mapping file (samples -> fastq)
$methodsfile     = "$projectdir/methods.txt";		        #-- File listing the  methods used and their citation info
$syslogfile      = "$projectdir/syslog";                        #-- Logging file
$contigsfna      = "$resultpath/01.$projectname.fasta";         #-- Contig file from assembly
$contigslen      = "$interdir/01.$projectname.lon";             #-- Length of each contig
$rnafile         = "$resultpath/02.$projectname.rnas";          #-- RNAs from barrnap
$trnafile        = "$resultpath/02.$projectname.trnas";         #-- tRNAs from aragorn
$gff_file        = "$resultpath/03.$projectname.gff";           #-- gff file from prodigal
$aafile          = "$resultpath/03.$projectname.faa";           #-- Aminoacid sequences for genes
$ntfile          = "$resultpath/03.$projectname.fna";           #-- Nucleotide sequences for genes
$taxdiamond      = "$interdir/04.$projectname.nr.diamond";      #-- Diamond result
$cogdiamond      = "$interdir/04.$projectname.eggnog.diamond";  #-- Diamond result, COGs
$keggdiamond     = "$interdir/04.$projectname.kegg.diamond";    #-- Diamond result, KEGG
$pfamhmmer       = "$interdir/05.$projectname.pfam.hmm";        #-- Hmmer result for Pfam
$fun3tax         = "$resultpath/06.$projectname.fun3.tax";      #-- Fun3 annotations, KEGG
$fun3kegg        = "$resultpath/07.$projectname.fun3.kegg";     #-- Fun3 annotations, KEGG
$fun3cog         = "$resultpath/07.$projectname.fun3.cog";      #-- Fun3 annotation, COGs
$fun3pfam        = "$resultpath/07.$projectname.fun3.pfam";     #-- Fun3 annotation, Pfams
$gff_file_blastx = "$resultpath/08.$projectname.gff";           #-- gff file from prodigal & blastx
$fun3tax_blastx  = "$resultpath/08.$projectname.fun3.tax";      #-- Fun3 annotations prodigal & blastx, KEGG
$fun3kegg_blastx = "$resultpath/08.$projectname.fun3.kegg";     #-- Fun3 annotations prodigal & blastx, KEGG
$fun3cog_blastx  = "$resultpath/08.$projectname.fun3.cog";      #-- Fun3 annotation prodigal & blastx, COGs
$fna_blastx      = "$interdir/08.$projectname.blastx.fna";      #-- Secuencias nt obtenidas por blastx
$allorfs         = "$tempdir/09.$projectname.allorfs";          #-- From summary_contigs.pl, allorfs file
$alllog          = "$interdir/09.$projectname.contiglog";       #-- From summary_contigs.pl, contiglog file (formerly alllog file)
$mapcountfile    = "$interdir/10.$projectname.mapcount";        #-- From mapsamples.pl, rpkm and coverage counts for all samples
$contigcov       = "$interdir/10.$projectname.contigcov";       #-- From mapbamsamples.pl, coverages of  for all samples
$mappingstat     = "$resultpath/10.$projectname.mappingstat";   #-- From mapsamples.pl, mapping statistics for all samples
$mcountfile      = "$resultpath/11.$projectname.mcount";        #-- From mcount.pl, abundances of all taxa
$mergedfile      = "$resultpath/13.$projectname.orftable";      #-- Gene table file
$bintax          = "$interdir/16.$projectname.bintax";          #-- From addtax2.pl
$checkmfile	 = "$interdir/17.$projectname.checkM";	#-- From checkm_batch.pl
$bincov          = "$interdir/18.$projectname.bincov";          #-- Coverage of bins, from getbins.pl
$bintable        = "$resultpath/18.$projectname.bintable";      #-- Mapping of contigs in bins, from getbins.pl
$contigsinbins   = "$interdir/18.$projectname.contigsinbins";   #-- Bin to which each contig belongs
$contigtable     = "$resultpath/19.$projectname.contigtable";   #-- From getcontigs.pl, contigs table
#-- Datafiles
$coglist   = "$extdatapath/coglist.txt";        #-- COG equivalence file (COGid -> Function -> Functional class)
$kegglist  = "$extdatapath/keggfun2.txt";       #-- KEGG equivalence file (KEGGid -> Function -> Functional class)
$pfamlist  = "$extdatapath/pfam.dat";           #-- PFAM equivalence file
$taxlist   = "$extdatapath/alltaxlist.txt";     #-- Tax equivalence file 
$nr_db     = "$databasepath/nr.dmnd";
$cog_db    = "$databasepath/eggnog";
$kegg_db   = "$databasepath/keggdb";
$lca_db    = "$databasepath/LCA_tax/taxid.db";
$bowtieref = "$datapath/$projectname.bowtie";   #-- Contigs formatted for Bowtie
$pfam_db   = "$databasepath/Pfam-A.hmm";
$mothur_r  = "$databasepath/silva.nr_v132.align";
$mothur_t  = "$databasepath/silva.nr_v132.tax";
#-- Variables
$blocksize       = NF;
$nodiamond       = 0;
$nocog           = 0;
$nokegg          = 0;
$nopfam          = 0;
$euknofilter     = 1;
$nobins          = 1;
$doublepass      = 1;
$norename        = 0;
$singletons      = 0;
$cleaning        = 0;
$cleaningoptions = "";
$mapper          = "bowtie";
$binners         = "concoct,metabat2";
$mapping_options = "";
#-- External software
$metabat_soft       = "metabat2";
$jgi_summ_soft      = "jgi_summarize_bam_contig_depths";
$maxbin_soft        = "$installpath/bin/MaxBin/run_MaxBin.pl";
$concoct_dir        = "$installpath/bin/CONCOCT-1.1.0";
$spades_soft        = "spades.py";
$barrnap_soft       = "$installpath/bin/barrnap";
$rdpclassifier_soft = "java -jar $installpath/lib/classifier/classifier.jar";
$bowtie2_build_soft = "python3 $installpath/bin/bowtie2/bowtie2-build";
$bowtie2_x_soft     = "$installpath/bin/bowtie2/bowtie2";
$bwa_soft           = "$installpath/bin/bwa";
$minimap2_soft      = "$installpath/bin/minimap2";
$samtools_soft      = "samtools";
$diamond_soft       = "$installpath/bin/diamond";
$hmmer_soft         = "$installpath/bin/hmmer/hmmsearch";
$megahit_soft       = "$installpath/bin/megahit/megahit";
$prinseq_soft       = "$installpath/bin/prinseq-lite.pl";
$prodigal_soft      = "$installpath/bin/prodigal";
$cdhit_soft         = "$installpath/bin/cd-hit-est";
$toamos_soft        = "$installpath/bin/AMOS/toAmos";
$minimus2_soft      = "$installpath/bin/AMOS/minimus2";
$checkm_soft        = "PATH=$installpath/bin:$installpath/bin/pplacer:$installpath/bin/hmmer:\$PATH $installpath/bin/checkm";
$minpath_soft       = "python3 $installpath/bin/MinPath1.4.py";
$canu_soft          = "$installpath/bin/canu-2.2/bin/canu";
$flye_soft          = "$installpath/bin/Flye-2.9/bin/flye";
$trimmomatic_soft   = "java -jar $installpath/bin/trimmomatic-0.38.jar";
$dastool_soft       = "LD_LIBRARY_PATH=$installpath/lib PATH=$installpath/bin:\$PATH $installpath/bin/DAS_Tool/DAS_Tool";
$kmerdb_soft        = "kmer-db";
$aragorn_soft       = "$installpath/bin/aragorn";
$mothur_soft        = "mothur";

#-- Options

$numthreads         = 8;
$mincontiglen       = 200;
$assembler          = "rnaspades";
$canumem            = NF;
$taxbinmode             = "s";

#-- New external database

$opt_db        = "/public/home/zhanglj/squeezemetatrans/db.list";