configfile.txt

# GENERAL
WORKDIR=$PWD                          # default: $PWD
WORKTMPDIR=/scratch/aims/$(basename $WORKDIR)  # default: /scratch/aims/$(basename $WORKDIR)
SCRIPTS=$PWD/scripts

# DATABASES
VIRREFSEQ=db/viral_refseq.faa
MARKERDB=db/20151230_holovir_markers.faa
SPROTDB=db/uniprot_sprot.fasta
SPROTKW=db/uniprot_sprot.keywords.txt.gz
EGGNOGDB=db/eggnog4.proteins.all.fa
NOG_MEMBERS=db/NOG.members.tsv.gz
FUNCCATEGORIES=db/eggnog4.functional_categories.txt

# CLUSTER
BLASTDBTMPDIR=/tmp/aims/db
LOCKDIR=/$PWD/locks

# PREPROCESS
PP_DATADIR=$WORKDIR/data
PP_DIR=$WORKDIR/00preprocess
PP_TMPDIR=$WORKTMPDIR/preprocess

# REFSEQ READS
RR_DATADIR=$PP_DIR/results
RR_DIR=$WORKDIR/01refseqreads
RR_TMPDIR=$WORKTMPDIR/refseqreads
RR_CHUNKSIZE=500 # default: 500

# MARKER READS
MR_DATADIR=$PP_DIR/results
MR_DIR=$WORKDIR/02markerreads
MR_TMPDIR=$WORKTMPDIR/markerreads
MR_CHUNKSIZE=500  # default: 500

# ASSEMBLY
AS_DATADIR=$WORKDIR/data
AS_DIR=$WORKDIR/03assembly

# GENE PREDICTION
GP_DATADIR=$AS_DIR/results
GP_DIR=$WORKDIR/04geneprediction

# REFSEQ GENES
RG_DATADIR=$GP_DIR/results
RG_DIR=$WORKDIR/05refseqgenes
RG_TMPDIR=$WORKTMPDIR/refseqgenes
RG_CHUNKSIZE=1000  # default: 1000

# MARKER GENES
MG_DATADIR=$GP_DIR/results
MG_DIR=$WORKDIR/06markergenes
MG_TMPDIR=$WORKTMPDIR/markergenes
MG_CHUNKSIZE=500  # default: 500

# SWISSPROT GENES
UNIPROT_SPROT_FASTA=ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
UNIPROT_SPROT_XML=ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz
SG_DATADIR=$GP_DIR/results
SG_DIR=$WORKDIR/07swissprotgenes
SG_TMPDIR=$WORKTMPDIR/swissprotgenes
SG_CHUNKSIZE=1000 # default: 1000

# EGGNOG GENES
EGGNOGDB_ONLINE=http://eggnogdb.embl.de/download/eggnog_4.1/eggnog4.proteins.all.fa.gz
NOG_MEMBERS_ONLINE=http://eggnogdb.embl.de/download/eggnog_4.1/data/NOG/NOG.members.tsv.gz
FUNCCATEGORIES_ONLINE=http://eggnogdb.embl.de/download/eggnog_4.1/eggnog4.functional_categories.txt
EG_DATADIR=$GP_DIR/results
EG_DIR=$WORKDIR/08eggnoggenes
EG_TMPDIR=$WORKTMPDIR/eggnoggenes
EG_CHUNKSIZE=200 # default: 200