interproscan package: add version 4.8, patch for version 5 (#12897)
This PR adds interproscan-4.8, which has a completely different build system than version 5. Note that this builds for running on a host as opposed to a queue system. I am fairly certain that a queue system can be configured later. This PR also adds a patch for intrproscan-5 to build when the user building the packages has a large GID by setting posix mode for tar.
This commit is contained in:
Glenn Johnson
Peter Scheibel
parent
c5860d89b7
commit
dd626a0f07
3 changed files with 222 additions and 3 deletions
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@ -0,0 +1,22 @@
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diff -ruN a/core/jms-implementation/pom.xml b/core/jms-implementation/pom.xml
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--- a/core/jms-implementation/pom.xml 2019-07-03 04:17:42.000000000 -0500
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+++ b/core/jms-implementation/pom.xml 2019-09-21 10:20:42.710868269 -0500
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@@ -275,6 +275,7 @@
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<descriptors>
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<descriptor>assembly.xml</descriptor>
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</descriptors>
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+ <tarLongFileMode>posix</tarLongFileMode>
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<finalName>interproscan-5</finalName>
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</configuration>
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<executions>
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diff -ruN a/core/precalcmatches/berkeley/pom.xml b/core/precalcmatches/berkeley/pom.xml
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--- a/core/precalcmatches/berkeley/pom.xml 2019-07-03 04:17:42.000000000 -0500
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+++ b/core/precalcmatches/berkeley/pom.xml 2019-09-21 10:21:16.874804845 -0500
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@@ -41,6 +41,7 @@
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<descriptors>
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<descriptor>assembly.xml</descriptor>
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</descriptors>
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+ <tarLongFileMode>posix</tarLongFileMode>
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<finalName>berkeley-db-builder</finalName>
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</configuration>
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<executions>
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@ -0,0 +1,165 @@
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--- a/Config.pl 2019-09-21 20:28:01.980128054 -0500
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+++ b/Config.pl 2019-09-21 21:45:50.926522289 -0500
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@@ -75,11 +75,12 @@
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close INS;
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}
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-$insDone = get_user_prompt('Reconfigure everything? (first time install)', $insDone, '(y|n)');
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+$insDone = 'y';
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$Tip = "!\n! InterProScan needs to know where it is installed and where perl is installed\n!";
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undef($set_path);
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+$set_path = 'y';
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while(!defined($set_path)){
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$set_path = get_user_prompt('Do you want to set paths to perl and the installation directory?', $insDone, 'y|n', $Tip);
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@@ -106,7 +107,7 @@
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$suggest_path = $HOME if($HOME ne "");
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chomp($suggest_path);
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- $install_path = get_user_prompt('Please enter the full path for the InterProScan installation', $suggest_path, '.+', $Tip);
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+ $install_path = $suggest_path;
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unless ( -d $install_path )
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{
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@@ -121,7 +122,7 @@
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#Setting the iprscan home installation path
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for(@homechange){
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my $file = $install_path . $ARG;
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- patch_file($file, "\\\$ENV{IPRSCAN_HOME}", "$install_path");
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+ patch_file($file, "\\\$ENV\\\{IPRSCAN_HOME\\\}", "$install_path");
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patch_file($file, "IPRSCAN_HOME", "$install_path", 1);
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}
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@@ -133,7 +134,7 @@
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undef($res);
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while(!defined($res)){
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- $res = get_user_prompt("Do you want to set another Perl command in place of [$PERL_CMD]?", 'n' , 'y|n');
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+ $res = $PERL_CMD;
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unless(defined($res)){
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print STDOUT "WARNING: The input is not valid must be \'y\' or \'n\', try again\n";
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undef($res);
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@@ -174,7 +175,7 @@
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unless(open(MOD, ">$PWD/test.pl")){
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die "FATAL: Could not open $PWD/test.pl in writing mode to test for presence of modules :$!\n";
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}
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- print MOD "#!$PERL_CMD\n";
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+ print MOD "#!/usr/bin/env perl\n";
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print MOD "use $ARG;\n";
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print MOD "1;\n";
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close MOD;
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@@ -203,7 +204,7 @@
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$Tip = "!\n! To cope with bulk jobs and to enable efficient parallelization, InterProScan splits input files\n"
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."! with FASTA formatted sequences into smaller parts (chunks). Default size is \"100\" sequences per chunk\n!";
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-$setcnk = get_user_prompt('Do you want to setup chunk size', $insDone, '(y|n)', $Tip);
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+$setcnk = 'y';
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my $chunkz;
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if ($setcnk eq "y")
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@@ -211,7 +212,7 @@
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$Tip = "!\n! Here you should specify the maximum number of sequences allowed in each part (chunk). Please note\n"
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."! it is not recommended to have more then 3000 chunks.\n!";
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- $chunkz = get_user_prompt('Enter chunk size', '100', '[0-9]+', $Tip);
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+ $chunkz = '100';
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}
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print STDOUT "\n";
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@@ -225,7 +226,7 @@
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my($maxinaa, $maxinnt, $maxlennt, $minlenaa, $minorflen, $cdntable) = (undef, undef, undef, undef, undef, undef);
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-my $setseq = get_user_prompt('Do you want to configure this?', $insDone, '(y|n)', $Tip);
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+my $setseq = 'y';
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if($setseq eq 'y'){
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$maxinaa = '1000';
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@@ -234,13 +235,6 @@
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$minlenaa = '5';
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$minorflen = '50';
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$cdntable = '0';
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-
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- $maxinaa = get_user_prompt('Enter the maximum number of input protein sequences allowed', $maxinaa, '\d+');
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- $maxinnt = get_user_prompt('Enter the maximum number of input nucleic sequences allowed', $maxinnt, '\d+');
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- $maxlennt = get_user_prompt('Enter the maximum length (in nucleic acids) for a nucleotide sequence', $maxlennt, '\d+');
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- $minlenaa = get_user_prompt('Enter the minimum length (in amino acids) for a protein sequence', $minlenaa, '\d+');
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- $minorflen = get_user_prompt('Enter the minimum allowed length of a translated orf', $minorflen, '\d+');
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- $cdntable = get_user_prompt('Enter the default codon table value to use to translate dna/rna in six frames', $cdntable, '\d+');
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}
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print STDOUT "\n";
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@@ -249,7 +243,7 @@
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."! set up a particular search tool against a database and how exactly that application will be configured to run\n"
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."! in this next section. You will configure the queue systems (if any) you will use, first\n!";
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-$applset = get_user_prompt('Do you want to setup applications (if you don\'t, no applications will be included in InterProScan by default)?', $insDone, '(y|n)', $Tip);
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+$applset = 'y';
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my @setAppl = ();
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if($applset eq "y"){
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@@ -258,7 +252,7 @@
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."! Currently, we mainly support LSF (which is used at EBI) however, we also provide configuration files for other systems\n"
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."! which are listed in the documentation\n!";
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- $UseQ = get_user_prompt('Do you wish to use a queue system?', 'n', '(y|n)', $Tip);
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+ $UseQ = 'n';
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$Qsys = undef;
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my $cluster = 'foo';
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@@ -395,7 +389,7 @@
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#Defining local host name and arch
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my $supported_arch = 'OSF1|IRIX64|Linux|SunOS|Darwin|AIX';
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- ($local_server = `hostname`);
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+ ($local_server = 'localhost');
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($local_arch = `uname`);
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($serv = $local_server);
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$local_server =~ s/\n//g;
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@@ -416,7 +410,7 @@
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my $rep = ($ARG eq "tmhmm" || $ARG eq "signalp" ? 'n' : 'y');
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$Tip = "! ".ucfirst($ARG) . " " . $appldesc->{$ARG};
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- my $useappl = get_user_prompt("Do you want to use $ARG ?", $rep, '(y|n)', $Tip);
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+ my $useappl = 'y';
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my $linkdone = "$HOME/bin/binaries";
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my $arch = `uname`;
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$arch =~ s/\n//g;
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@@ -502,7 +496,7 @@
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SERVER : while(!defined($res_server)){
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- $res_server = get_user_prompt("\nPlease enter the execution host name of $ARG (or if you want to run locally, enter \'localhost\')", $serv, '\S+');
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+ $res_server = 'localhost';
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chomp($res_server);
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if($local_server ne $res_server){
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# rsh command has different behavior depending on the shell type.
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@@ -658,7 +652,7 @@
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$Tip = "!\n! You can specify an email address for the administrator. By default it will be you ($ENV{USER})\n"
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."! Administrators receive an email when a problem occurs in InterProScan.\n!";
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- $user = get_user_prompt("Do you want to set an administrator email address?", 'y', 'y|n', $Tip);
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+ $user = 'n';
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if($user eq 'y'){
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$user = get_user_prompt("Please enter the email address of the administrator:", '', '[\w\.\-]+\@[\w\.\-]+');
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}else{
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@@ -735,7 +729,7 @@
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$Tip = "!\n! InterProScan can be launched through a web interface. It can also be launched through secure HTTP (https)\n!";
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-my $useWeb = get_user_prompt("Do you want to run InterProScan using a web interface?", 'n', 'y|n', $Tip);
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+my $useWeb = 'n';
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my $HTTPProto;
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if($useWeb eq 'y'){
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@@ -816,7 +810,7 @@
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$Tip = "!\n! We would appreciate it if you would register your installation of InterProScan. This will allow us to notify you\n"
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."! of bug fixes and new releases of the software. We will not use your email address for any other purpose.\n!";
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-my $register = get_user_prompt("Would you like to register InterProScan?", $insDone, '(y|n)', $Tip);
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+my $register = 'n';
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if ($register eq "y")
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{
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my $org_name = get_user_prompt("What is the name of your organization?", '', '\S+');
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@ -16,11 +16,30 @@ class Interproscan(Package):
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url = "https://github.com/ebi-pf-team/interproscan/archive/5.36-75.0.tar.gz"
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url = "https://github.com/ebi-pf-team/interproscan/archive/5.36-75.0.tar.gz"
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version('5.36-75.0', sha256='383d7431e47c985056c856ceb6d4dcf7ed2559a4a3d5c210c01ce3975875addb')
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version('5.36-75.0', sha256='383d7431e47c985056c856ceb6d4dcf7ed2559a4a3d5c210c01ce3975875addb')
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version('4.8',
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sha256='f1cb0ae1218eb05ed59ad7f94883f474eb9a6185a56ad3a93a364acb73506a3f',
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url='ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/4/RELEASE/4.8/iprscan_v4.8.tar.gz')
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depends_on('java@8.0:8.9', type=('build', 'run'))
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resource(
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depends_on('maven', type='build')
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when='@:4.8',
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name='binaries',
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url="http://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/BIN/4.x/iprscan_bin4.x_Linux64.tar.gz",
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sha256='551610a4682b112522f3ded5268f76ba9a47399a72e726fafb17cc938a50e7ee',
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)
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depends_on('java@8.0:8.9', when='@5:', type=('build', 'run'))
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depends_on('maven', when='@5:', type='build')
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depends_on('python@3:', when='@5:', type=('build', 'run'))
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depends_on('perl@5:', type=('build', 'run'))
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depends_on('perl@5:', type=('build', 'run'))
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depends_on('python@3:', type=('build', 'run'))
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depends_on('perl-cgi', when='@:4.8', type=('build', 'run'))
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depends_on('perl-mailtools', when='@:4.8', type=('build', 'run'))
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depends_on('perl-xml-quote', when='@:4.8', type=('build', 'run'))
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depends_on('perl-xml-parser', when='@:4.8', type=('build', 'run'))
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depends_on('perl-io-string', when='@:4.8', type=('build', 'run'))
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depends_on('perl-io-stringy', when='@:4.8', type=('build', 'run'))
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patch('large-gid.patch', when='@5:')
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patch('non-interactive.patch', when='@:4.8')
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def install(self, spec, prefix):
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def install(self, spec, prefix):
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with working_dir('core'):
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with working_dir('core'):
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@ -31,3 +50,16 @@ def install(self, spec, prefix):
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# link the main shell script into the PATH
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# link the main shell script into the PATH
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ips_bin_suffix = 'core/jms-implementation/target/interproscan-5-dist'
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ips_bin_suffix = 'core/jms-implementation/target/interproscan-5-dist'
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symlink(join_path(prefix, ips_bin_suffix), prefix.bin)
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symlink(join_path(prefix, ips_bin_suffix), prefix.bin)
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@when('@:4.8')
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def install(self, spec, prefix):
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perl = which('perl')
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src = join_path(self.stage.source_path, 'iprscan', 'bin', 'Linux')
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dst = join_path(self.stage.source_path, 'bin', 'binaries')
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force_symlink(src, dst)
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install_tree('.', prefix)
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with working_dir(prefix):
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perl('Config.pl')
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