Here is the YAML for the default configurations of the NewPred services, that are currently live. This defines the set of variables that must be configured and their literal names. For now you must ensure that there are no trailing white spaces in the variables provided. The name specified MUST be the name of the configuration as added

seqJob

UnfilteredBlastDB: /webdata/data/current/blast/db/uniref90.fasta
program_ffpred: "0"
netoglyc: /webdata/binaries/current/netOglyc-3.1d/netOglyc
BlastPlusBin: /webdata/binaries/current/ncbi-blast-2.2.25+-src/c++/GCC412-Debug64/bin/psiblast
prob2Html_dom: /webdata/binaries/current/psipred/bin/prob2htm5
gettmimage: /webdata/binaries/current/FFPred/getTmIMAGE.pl
GsBin: gs
HHSeqDB: /webdata/data/current/hhblits/pdb70
Mempack: /webdata/binaries/current/mempack/run_mempack.pl
TempDir: /webdata/tmp/NewPredServer/
database: nonrucl
PSIPRED_DATABASES: /webdata/data/current/psipred/data/
pseudo_bas_dom: /webdata/binaries/current/psipred/bin/pseudo_bas_dom
hhsearch: /webdata/binaries/current/HHblits/hhsearch
include_sec_structure_plot: "yes"
complex_filter_setting: "true"
Dformat: /webdata/binaries/current/disopred/bin/disopred
parseDS: /webdata/binaries/current/dompred/parseDS_plus.pl
PsiBlastBin: /webdata/binaries/current/blast/bin/blastpgp
DOM_TDB_DIR: /webdata/data/cath_tdb/
Ps2PdfBin: ps2pdf
GraphicsBinaries: /webdata/binaries/current/psipred/gra/
e_value: "0.01"
eValueThreshold: "0.00005"
ModArch: /webdata/binaries/current/modeller9.10/lib/x86_64-intel8/
qmodcheck: /webdata/binaries/current/HHblits/qmodcheck_mainens
result_filter_setting: CERT
program_disopred: "0"
IdThresh: "40.0"
MakeBlastDBBin: /webdata/binaries/current/ncbi-blast-2.2.25+-src/c++/GCC412-Debug64/bin/makeblastdb
membrane_filter_setting: "false"
program_domthreader: "0"
buildMultiAlignment: /webdata/binaries/current/psipred/bin/build_multi_alignment.pl
program_dompred: "0"
PsipassBin: /webdata/binaries/current/psipred/bin/psipass2
PDBAA_DB: /webdata/data/current/blast/db/pdbaa
AllCut: /webdata/data/current/dompred/All_cut3
reformat: /webdata/binaries/current/FFPred/reFormat.pl
getschematic: /webdata/binaries/current/FFPred/getSchematic.pl
coil_filter_setting: "false"
CSA: /webdata/data/current/CSA/CSA_2_2_12.dat
TS_MGT_MIN_MIN_SCORE: "35"
DownloadPath: /home/rails/NewPred/public/genthreader_output/
Gnuplot: /usr/bin/gnuplot
MODELLER_BIN: /webdata/binaries/current/modeller9.10/bin/mod9.10
program_mempack: "0"
addss: /webdata/binaries/current/HHblits/addss.pl
PDB_ROOT: /webdata/data/pdb/
secondary_structure_prediction: "true"
MemsatSvm: /webdata/binaries/current/memsat-svm-pore/run_memsat-svm.pl
epest: /webdata/binaries/current/EMBOSS-6.4.0/emboss/epestfind
PSIPRED_WEIGHTS_DIR: /webdata/data/current/psipred/weights/
Dompred_blast_db: /webdata/data/current/dompred/uniref90_PfamA_plus
genAlignmentAnnotator: /webdata/binaries/current/GenAlignmentHandler/main.rb
nofragblastplusDB: /webdata/data/current/blast/db/plus/uniref90_nofrag
PfiltNormalBin: /webdata/binaries/current/psipred/bin/pfilt
SSPRedAvBin: /webdata/binaries/current/psipred/bin/psipred
program_genthreader: "0"
program_mgenthreader: "0"
sortprob_bas: /webdata/binaries/current/psipred/bin/sortprob_bas
diso_false_positive_setting: "2"
program_bioserf: "0"
processvm: /webdata/binaries/current/FFPred/FFPred.pl
LibSvmDir: /webdata/binaries/current/libsvm-3.11/
hhblits: /webdata/binaries/current/HHblits/hhblits
coils: /webdata/binaries/current/coils/ncoils
ChkParseBin: /webdata/binaries/current/psipred/bin/chkparse
display_psipred: "yes"
HHPdbDB: /webdata/data/current/hhblits/pdb70
JavaPath: /webdata/binaries/current/jdk1.6.0_14/bin/
features.pl: /webdata/binaries/current/FFPred/featurama/features.pl
hhmakemodel: /webdata/binaries/current/HHblits/hhmakemodel_cbmain.pl
rewrite_ann: /webdata/binaries/current/GenAlignmentHandler/rewrite_ann.pl
PfiltPipeBin: /webdata/binaries/current/psipred/bin/pfilt_pipe
netphos: /webdata/binaries/current/ape-1.0/ape
MempackDir: /webdata/binaries/current/mempack/
psipblast_output_option: opnone
netnglyc: /webdata/binaries/current/netNglyc-1.0c/netNglyc
MakematBin: /webdata/binaries/current/blast/bin/makemat
THREAD_DIR: /webdata/binaries/current/psipred/
msa_control_setting: all
prob2Html: /webdata/binaries/current/psipred/bin/prob2htm4
msa_input: "0"
FilteredBlastPlusDB: /webdata/data/current/blast/db/plus/uniref90_filt
perform_psiblast: "yes"
ModLib: /webdata/binaries/current/modeller9.10/modlib/
tmjury: /webdata/binaries/current/HHblits/tmjury3d_mq_modeller_threadsafe
dompred_data: /webdata/data/current/dompred/
MemsatDir: /webdata/binaries/current/memsat-svm-pore/
predict_contacts: /webdata/binaries/current/psipred/bin/predict_contacts_web.pl
psi_blast_iterations: "5"
CoilsDir: /webdata/binaries/current/coils/
program_svmmemsat: "0"
FilteredBlastDB: /webdata/data/current/blast/db/uniref90_filt
HHLIB: /webdata/binaries/current/HHblits/hhsuite/lib/hh
Seq2MtxBin: /webdata/binaries/current/psipred/bin/seq2mtx
perform_domssea: "yes"
sortprob_dom: /webdata/binaries/current/psipred/bin/svm_prob_dom
UnilteredBlastPlusDB: /webdata/data/current/blast/db/plus/uniref90_nofrag
DisoPredWeightsDir: /webdata/binaries/current/disopred/data/
TDB_DIR: /webdata/data/tdb/
pseudo_bas: /webdata/binaries/current/psipred/bin/pseudo_bas
program_psipred: "0"
psort: /webdata/binaries/current/WoLFPSORT_package_v0.2/bin/runWolfPsortSummary
SigP: /webdata/binaries/current/signalp-4.0/signalp
false_positive_setting: "2"
features: /webdata/binaries/current/SeqFeat/features
perl: /usr/bin/perl

StructJob

fasta_pdb: /webdata/binaries/current/metsite/bin/fasta_pdbv3.pl
splitPDB: /webdata/binaries/current/hs_pred/split_pdb.pl
blastdb: /webdata/data/current/blast/db/uniref90_filt
HBplus: /webdata/binaries/current/hs_pred/hbplus
HSPred: /webdata/binaries/current/hs_pred/hs-pred_v0_1.pl
makeTDB: /webdata/data/autoupdate/make_tdb.pl
ChkParse: /webdata/data/autoupdate/chkparse
dssp: /webdata/binaries/current/metsite/bin/dssp
PDB: /webdata/tmp/NewPredServer/
ParseSource: /webdata/data/autoupdate/bin/parse_source
metsite_data: /webdata/data/current/metsite/
tdbPsiBlast: /webdata/binaries/current/ncbi-blast-2.2.25+-src/c++/GCC412-Debug64/bin/psiblast
HsDataDir: /webdata/binaries/current/hs_pred/
DsspDir: /webdata/tmp/NewPredServer/
TempDir: /webdata/tmp/NewPredServer/
CATHAlignDir: /webdata/data/cath_pdb/v3_3_0-structural_alignments/
MTXpro: /webdata/binaries/current/metsite/bin/mtx_pro
cleanExpect: /webdata/binaries/current/hs_pred/clean_expect.pl
tdbBlastDB: /webdata/data/current/blast/db/plus/uniref90_filt
checkTdbPdb: /webdata/data/autoupdate/check_tdb_pdb.pl
CATHDB: /webdata/data/cath_pdb/plus/CathDomainSeqs.S100.ATOM.annotated
TCOffeeBin: /webdata/binaries/current/T-COFFEE_distribution_Version_8.91/bin/binaries/linux/t_coffee
seq2mtx: /webdata/binaries/current/metsite/bin/seq2mtx
checkChains: /webdata/binaries/current/hs_pred/checkchains.pl
seedsitefind: /webdata/binaries/current/metsite/bin/seedSiteFind
MetPred: /webdata/binaries/current/metsite/bin/MetPred
makemat: /webdata/binaries/current/blast/bin/makemat
psiblast: /webdata/binaries/current/blast/bin/blastpgp
metCheckChains: /webdata/binaries/current/metsite/bin/checkchains_metsite.pl

NewPred

PSIPRED_DATABASES: /var/www/cgi-bin/psipred/latest_tdb/
TDB_DIR: /var/www/cgi-bin/psipred/latest_tdb/
BlastDB: /var/www/cgi-bin/psipred/data/unifilt
HHPdbDB: /var/www/cgi-bin/psipred/data/pdb70
complex_filter_setting: "true"
membrane_filter_setting: "true"
TempDir: /var/tmp/
HHLIB: /var/www/cgi-bin/psipred/hhsuite/lib/hh
IdThresh: "40.0"
THREAD_DIR: /var/www/cgi-bin/psipred/latest_tdb/
PSIPRED_WEIGHTS_DIR: /var/www/cgi-bin/psipred/
MODELLER_BIN: /home/casp/BioSerf_1_1/modeller-9v8/bin/mod9v8
HHSeqDB: /var/www/cgi-bin/psipred/data/pdb70
coil_filter_setting: "true"
DB_ROOT: /var/www/cgi-bin/psipred/autoupdate/pdb/
PDBAA_DB: /home/casp/BioSerf_1_1/pdbaa/pdb_aa.fasta
BlastBinDir: /home/casp/BioSerf_1_1/ncbi-blast-2.2.26+/bin/
eValueThreshold: "0.00005"
BinDir: /var/www/cgi-bin/psipred/bin/
PSIBlastBin: /var/www/cgi-bin/psipred/bin/

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« This page (revision-1) was last changed on 11-Feb-2013 15:47 by UnknownAuthor