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interproscan package: add version 4.8, patch for version 5 (#12897)

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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 2019-09-25 21:04:57 -05:00 committed by Peter Scheibel
parent c5860d89b7
commit dd626a0f07
3 changed files with 222 additions and 3 deletions
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22
var/spack/repos/builtin/packages/interproscan/large-gid.patch Normal file
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@ -0,0 +1,22 @@
diff -ruN a/core/jms-implementation/pom.xml b/core/jms-implementation/pom.xml
--- a/core/jms-implementation/pom.xml 2019-07-03 04:17:42.000000000 -0500
+++ b/core/jms-implementation/pom.xml 2019-09-21 10:20:42.710868269 -0500
@@ -275,6 +275,7 @@
<descriptors>
<descriptor>assembly.xml</descriptor>
</descriptors>
+ <tarLongFileMode>posix</tarLongFileMode>
<finalName>interproscan-5</finalName>
</configuration>
<executions>
diff -ruN a/core/precalcmatches/berkeley/pom.xml b/core/precalcmatches/berkeley/pom.xml
--- a/core/precalcmatches/berkeley/pom.xml 2019-07-03 04:17:42.000000000 -0500
+++ b/core/precalcmatches/berkeley/pom.xml 2019-09-21 10:21:16.874804845 -0500
@@ -41,6 +41,7 @@
<descriptors>
<descriptor>assembly.xml</descriptor>
</descriptors>
+ <tarLongFileMode>posix</tarLongFileMode>
<finalName>berkeley-db-builder</finalName>
</configuration>
<executions>

165
var/spack/repos/builtin/packages/interproscan/non-interactive.patch Normal file
View file

@ -0,0 +1,165 @@
--- a/Config.pl 2019-09-21 20:28:01.980128054 -0500
+++ b/Config.pl 2019-09-21 21:45:50.926522289 -0500
@@ -75,11 +75,12 @@
close INS;
}
-$insDone = get_user_prompt('Reconfigure everything? (first time install)', $insDone, '(y|n)');
+$insDone = 'y';
$Tip = "!\n! InterProScan needs to know where it is installed and where perl is installed\n!";
undef($set_path);
+$set_path = 'y';
while(!defined($set_path)){
$set_path = get_user_prompt('Do you want to set paths to perl and the installation directory?', $insDone, 'y|n', $Tip);
@@ -106,7 +107,7 @@
$suggest_path = $HOME if($HOME ne "");
chomp($suggest_path);
- $install_path = get_user_prompt('Please enter the full path for the InterProScan installation', $suggest_path, '.+', $Tip);
+ $install_path = $suggest_path;
unless ( -d $install_path )
{
@@ -121,7 +122,7 @@
#Setting the iprscan home installation path
for(@homechange){
my $file = $install_path . $ARG;
- patch_file($file, "\\\$ENV{IPRSCAN_HOME}", "$install_path");
+ patch_file($file, "\\\$ENV\\\{IPRSCAN_HOME\\\}", "$install_path");
patch_file($file, "IPRSCAN_HOME", "$install_path", 1);
}
@@ -133,7 +134,7 @@
undef($res);
while(!defined($res)){
- $res = get_user_prompt("Do you want to set another Perl command in place of [$PERL_CMD]?", 'n' , 'y|n');
+ $res = $PERL_CMD;
unless(defined($res)){
print STDOUT "WARNING: The input is not valid must be \'y\' or \'n\', try again\n";
undef($res);
@@ -174,7 +175,7 @@
unless(open(MOD, ">$PWD/test.pl")){
die "FATAL: Could not open $PWD/test.pl in writing mode to test for presence of modules :$!\n";
}
- print MOD "#!$PERL_CMD\n";
+ print MOD "#!/usr/bin/env perl\n";
print MOD "use $ARG;\n";
print MOD "1;\n";
close MOD;
@@ -203,7 +204,7 @@
$Tip = "!\n! To cope with bulk jobs and to enable efficient parallelization, InterProScan splits input files\n"
."! with FASTA formatted sequences into smaller parts (chunks). Default size is \"100\" sequences per chunk\n!";
-$setcnk = get_user_prompt('Do you want to setup chunk size', $insDone, '(y|n)', $Tip);
+$setcnk = 'y';
my $chunkz;
if ($setcnk eq "y")
@@ -211,7 +212,7 @@
$Tip = "!\n! Here you should specify the maximum number of sequences allowed in each part (chunk). Please note\n"
."! it is not recommended to have more then 3000 chunks.\n!";
- $chunkz = get_user_prompt('Enter chunk size', '100', '[0-9]+', $Tip);
+ $chunkz = '100';
}
print STDOUT "\n";
@@ -225,7 +226,7 @@
my($maxinaa, $maxinnt, $maxlennt, $minlenaa, $minorflen, $cdntable) = (undef, undef, undef, undef, undef, undef);
-my $setseq = get_user_prompt('Do you want to configure this?', $insDone, '(y|n)', $Tip);
+my $setseq = 'y';
if($setseq eq 'y'){
$maxinaa = '1000';
@@ -234,13 +235,6 @@
$minlenaa = '5';
$minorflen = '50';
$cdntable = '0';
-
- $maxinaa = get_user_prompt('Enter the maximum number of input protein sequences allowed', $maxinaa, '\d+');
- $maxinnt = get_user_prompt('Enter the maximum number of input nucleic sequences allowed', $maxinnt, '\d+');
- $maxlennt = get_user_prompt('Enter the maximum length (in nucleic acids) for a nucleotide sequence', $maxlennt, '\d+');
- $minlenaa = get_user_prompt('Enter the minimum length (in amino acids) for a protein sequence', $minlenaa, '\d+');
- $minorflen = get_user_prompt('Enter the minimum allowed length of a translated orf', $minorflen, '\d+');
- $cdntable = get_user_prompt('Enter the default codon table value to use to translate dna/rna in six frames', $cdntable, '\d+');
}
print STDOUT "\n";
@@ -249,7 +243,7 @@
."! set up a particular search tool against a database and how exactly that application will be configured to run\n"
."! in this next section. You will configure the queue systems (if any) you will use, first\n!";
-$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)', $Tip);
+$applset = 'y';
my @setAppl = ();
if($applset eq "y"){
@@ -258,7 +252,7 @@
."! Currently, we mainly support LSF (which is used at EBI) however, we also provide configuration files for other systems\n"
."! which are listed in the documentation\n!";
- $UseQ = get_user_prompt('Do you wish to use a queue system?', 'n', '(y|n)', $Tip);
+ $UseQ = 'n';
$Qsys = undef;
my $cluster = 'foo';
@@ -395,7 +389,7 @@
#Defining local host name and arch
my $supported_arch = 'OSF1|IRIX64|Linux|SunOS|Darwin|AIX';
- ($local_server = `hostname`);
+ ($local_server = 'localhost');
($local_arch = `uname`);
($serv = $local_server);
$local_server =~ s/\n//g;
@@ -416,7 +410,7 @@
my $rep = ($ARG eq "tmhmm" || $ARG eq "signalp" ? 'n' : 'y');
$Tip = "! ".ucfirst($ARG) . " " . $appldesc->{$ARG};
- my $useappl = get_user_prompt("Do you want to use $ARG ?", $rep, '(y|n)', $Tip);
+ my $useappl = 'y';
my $linkdone = "$HOME/bin/binaries";
my $arch = `uname`;
$arch =~ s/\n//g;
@@ -502,7 +496,7 @@
SERVER : while(!defined($res_server)){
- $res_server = get_user_prompt("\nPlease enter the execution host name of $ARG (or if you want to run locally, enter \'localhost\')", $serv, '\S+');
+ $res_server = 'localhost';
chomp($res_server);
if($local_server ne $res_server){
# rsh command has different behavior depending on the shell type.
@@ -658,7 +652,7 @@
$Tip = "!\n! You can specify an email address for the administrator. By default it will be you ($ENV{USER})\n"
."! Administrators receive an email when a problem occurs in InterProScan.\n!";
- $user = get_user_prompt("Do you want to set an administrator email address?", 'y', 'y|n', $Tip);
+ $user = 'n';
if($user eq 'y'){
$user = get_user_prompt("Please enter the email address of the administrator:", '', '[\w\.\-]+\@[\w\.\-]+');
}else{
@@ -735,7 +729,7 @@
$Tip = "!\n! InterProScan can be launched through a web interface. It can also be launched through secure HTTP (https)\n!";
-my $useWeb = get_user_prompt("Do you want to run InterProScan using a web interface?", 'n', 'y|n', $Tip);
+my $useWeb = 'n';
my $HTTPProto;
if($useWeb eq 'y'){
@@ -816,7 +810,7 @@
$Tip = "!\n! We would appreciate it if you would register your installation of InterProScan. This will allow us to notify you\n"
."! of bug fixes and new releases of the software. We will not use your email address for any other purpose.\n!";
-my $register = get_user_prompt("Would you like to register InterProScan?", $insDone, '(y|n)', $Tip);
+my $register = 'n';
if ($register eq "y")
{
my $org_name = get_user_prompt("What is the name of your organization?", '', '\S+');

38
var/spack/repos/builtin/packages/interproscan/package.py
View file

@ -16,11 +16,30 @@ class Interproscan(Package):
url = "https://github.com/ebi-pf-team/interproscan/archive/5.36-75.0.tar.gz"
version('5.36-75.0', sha256='383d7431e47c985056c856ceb6d4dcf7ed2559a4a3d5c210c01ce3975875addb')
version('4.8',
sha256='f1cb0ae1218eb05ed59ad7f94883f474eb9a6185a56ad3a93a364acb73506a3f',
url='ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/4/RELEASE/4.8/iprscan_v4.8.tar.gz')
depends_on('java@8.0:8.9', type=('build', 'run'))
depends_on('maven', type='build')
resource(
when='@:4.8',
name='binaries',
url="http://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/BIN/4.x/iprscan_bin4.x_Linux64.tar.gz",
sha256='551610a4682b112522f3ded5268f76ba9a47399a72e726fafb17cc938a50e7ee',
)
depends_on('java@8.0:8.9', when='@5:', type=('build', 'run'))
depends_on('maven', when='@5:', type='build')
depends_on('python@3:', when='@5:', type=('build', 'run'))
depends_on('perl@5:', type=('build', 'run'))
depends_on('python@3:', type=('build', 'run'))
depends_on('perl-cgi', when='@:4.8', type=('build', 'run'))
depends_on('perl-mailtools', when='@:4.8', type=('build', 'run'))
depends_on('perl-xml-quote', when='@:4.8', type=('build', 'run'))
depends_on('perl-xml-parser', when='@:4.8', type=('build', 'run'))
depends_on('perl-io-string', when='@:4.8', type=('build', 'run'))
depends_on('perl-io-stringy', when='@:4.8', type=('build', 'run'))
patch('large-gid.patch', when='@5:')
patch('non-interactive.patch', when='@:4.8')
def install(self, spec, prefix):
with working_dir('core'):
@ -31,3 +50,16 @@ def install(self, spec, prefix):
# link the main shell script into the PATH
ips_bin_suffix = 'core/jms-implementation/target/interproscan-5-dist'
symlink(join_path(prefix, ips_bin_suffix), prefix.bin)
@when('@:4.8')
def install(self, spec, prefix):
perl = which('perl')
src = join_path(self.stage.source_path, 'iprscan', 'bin', 'Linux')
dst = join_path(self.stage.source_path, 'bin', 'binaries')
force_symlink(src, dst)
install_tree('.', prefix)
with working_dir(prefix):
perl('Config.pl')