diff --git a/core/jms-implementation/support-mini-x86-32/bin/pirsf/3.10/pirsf.pl b/core/jms-implementation/support-mini-x86-32/bin/pirsf/3.10/pirsf.pl index 7a866a43c6..bcf4a6cd8d 100755 --- a/core/jms-implementation/support-mini-x86-32/bin/pirsf/3.10/pirsf.pl +++ b/core/jms-implementation/support-mini-x86-32/bin/pirsf/3.10/pirsf.pl @@ -64,7 +64,7 @@ # Main body # Check that the hmm files have been properly pressed -PIRSF::checkHmmFiles($sf_hmm, $hmmer_path); +# PIRSF::checkHmmFiles($sf_hmm, $hmmer_path); # Read the PIRSF data file. my ($pirsf_data, $children) = PIRSF::read_pirsf_dat($pirsf_dat); diff --git a/core/jms-implementation/support-mini-x86-32/data/pirsf/3.10/sf_hmm_all.h3f b/core/jms-implementation/support-mini-x86-32/data/pirsf/3.10/sf_hmm_all.h3f new file mode 100644 index 0000000000..e03012eb9a Binary files /dev/null and b/core/jms-implementation/support-mini-x86-32/data/pirsf/3.10/sf_hmm_all.h3f differ diff --git a/core/jms-implementation/support-mini-x86-32/data/pirsf/3.10/sf_hmm_all.h3i b/core/jms-implementation/support-mini-x86-32/data/pirsf/3.10/sf_hmm_all.h3i new file mode 100644 index 0000000000..c353fdface Binary files /dev/null and b/core/jms-implementation/support-mini-x86-32/data/pirsf/3.10/sf_hmm_all.h3i differ diff --git a/core/jms-implementation/support-mini-x86-32/data/pirsf/3.10/sf_hmm_all.h3m b/core/jms-implementation/support-mini-x86-32/data/pirsf/3.10/sf_hmm_all.h3m new file mode 100644 index 0000000000..5fabfee384 Binary files /dev/null and b/core/jms-implementation/support-mini-x86-32/data/pirsf/3.10/sf_hmm_all.h3m differ diff --git a/core/jms-implementation/support-mini-x86-32/data/pirsf/3.10/sf_hmm_all.h3p b/core/jms-implementation/support-mini-x86-32/data/pirsf/3.10/sf_hmm_all.h3p new file mode 100644 index 0000000000..eca356ee86 Binary files /dev/null and b/core/jms-implementation/support-mini-x86-32/data/pirsf/3.10/sf_hmm_all.h3p differ diff --git a/core/jms-implementation/support-mini-x86-32/data/superfamily/1.75/hmmlib_1.75.h3f b/core/jms-implementation/support-mini-x86-32/data/superfamily/1.75/hmmlib_1.75.h3f new file mode 100644 index 0000000000..6ea00aa3d9 Binary files /dev/null and b/core/jms-implementation/support-mini-x86-32/data/superfamily/1.75/hmmlib_1.75.h3f differ diff --git a/core/jms-implementation/support-mini-x86-32/data/superfamily/1.75/hmmlib_1.75.h3i b/core/jms-implementation/support-mini-x86-32/data/superfamily/1.75/hmmlib_1.75.h3i new file mode 100644 index 0000000000..6cca06c76c Binary files /dev/null and b/core/jms-implementation/support-mini-x86-32/data/superfamily/1.75/hmmlib_1.75.h3i differ diff --git a/core/jms-implementation/support-mini-x86-32/data/superfamily/1.75/hmmlib_1.75.h3m b/core/jms-implementation/support-mini-x86-32/data/superfamily/1.75/hmmlib_1.75.h3m new file mode 100644 index 0000000000..be32795ab6 Binary files /dev/null and b/core/jms-implementation/support-mini-x86-32/data/superfamily/1.75/hmmlib_1.75.h3m differ diff --git a/core/jms-implementation/support-mini-x86-32/data/superfamily/1.75/hmmlib_1.75.h3p b/core/jms-implementation/support-mini-x86-32/data/superfamily/1.75/hmmlib_1.75.h3p new file mode 100644 index 0000000000..d453f86e92 Binary files /dev/null and b/core/jms-implementation/support-mini-x86-32/data/superfamily/1.75/hmmlib_1.75.h3p differ diff --git a/core/jms-implementation/support-mini-x86-32/interproscan.sh b/core/jms-implementation/support-mini-x86-32/interproscan.sh index f3f6691b0e..8c5533fc57 100644 --- a/core/jms-implementation/support-mini-x86-32/interproscan.sh +++ b/core/jms-implementation/support-mini-x86-32/interproscan.sh @@ -49,11 +49,6 @@ then exit 1 fi -if ! python3 setup.py "$PROPERTIES" -then - exit 1 -fi - "$JAVA" \ -XX:ParallelGCThreads=8 \ -Xms2028M -Xmx9216M \ diff --git a/core/jms-implementation/support-mini-x86-32/setup.py b/core/jms-implementation/support-mini-x86-32/setup.py deleted file mode 100755 index 2006e6fe91..0000000000 --- a/core/jms-implementation/support-mini-x86-32/setup.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python3 - -import argparse -import glob -import os -import subprocess as sp -import sys - - -PROPERTIES="interproscan.properties" - - -def load_properties(file, properties): - with open(file, "rt") as fh: - for line in map(str.strip, fh): - if not line or line[0] == "#": - continue - - fields = line.split("=", 1) - if len(fields) == 2: - key = fields[0].strip() - value = fields[1].strip() - properties[key] = value - - try: - bin_dir = properties["bin.directory"] - data_dir = properties["data.directory"] - except KeyError: - return - - for key, value in properties.items(): - if "${bin.directory}" in value: - value = value.replace("${bin.directory}", bin_dir) - - if "${data.directory}" in value: - value = value.replace("${data.directory}", data_dir) - - properties[key] = value - - -def is_ready(hmmfile): - for ext in [".h3m", ".h3i", ".h3f", ".h3p"]: - if not os.path.isfile(hmmfile + ext): - return False - - return True - - -def hmmpress(binary, force, database): - if force: - cmd = [binary, "-f", database] - else: - cmd = [binary, database] - - proc = sp.Popen(cmd, stdout=sp.PIPE, stderr=sp.PIPE) - outs, errs = proc.communicate() - - if proc.returncode != 0: - sys.stderr.write(errs.decode()) - sys.exit(1) - - -def realpath(path): - return os.path.realpath(os.path.expanduser(path)) - - -def main(): - parser = argparse.ArgumentParser(description="index HMM databases") - parser.add_argument("properties", help="InterProScan properties file") - parser.add_argument("-f", "--force", action="store_true", - help="re-index all HMM databases (default: off)") - args = parser.parse_args() - - properties = {} - load_properties(PROPERTIES, properties) - - if realpath(args.properties) != realpath(PROPERTIES): - load_properties(args.properties, properties) - - ignore = {"binary.tmhmm.path", "funfam.hmm.path", "smart.hmm.path"} - for key, path in properties.items(): - if "hmm.path" in key and key not in ignore: - bin_key = "binary.hmmer3.path" - - if os.path.isfile(path): - hmmfiles = [path] - else: - hmmfiles = glob.iglob(os.path.join(path, "**", "*.hmm"), - recursive=True) - - for hmmfile in hmmfiles: - if args.force or not is_ready(hmmfile): - try: - bin_path = os.path.join(properties[bin_key], "hmmpress") - except KeyError: - continue - else: - hmmpress(bin_path, args.force, hmmfile) - - -if __name__ == '__main__': - main()