hlrs-software-stack/spack
7
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity

fastqc: add 0.12.1, update patch files (#37934)

Browse source 
* fastqc: add 0.12.1

* fastqc: add 0.12.1

* Update var/spack/repos/builtin/packages/fastqc/package.py

Yeah, had considered doing the same, I'd just opted to maintain the status quo. All good.

Co-authored-by: Alec Scott <alec@bcs.sh>

* Update package.py

Style fiddles to make the bot contented.

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Alec Scott <alec@bcs.sh>
This commit is contained in:
George Young 2023-06-05 16:07:51 +01:00 committed by GitHub
parent d6765f66ae
commit 110f836927
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
3 changed files with 40 additions and 3 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

0
var/spack/repos/builtin/packages/fastqc/fastqc.patch → var/spack/repos/builtin/packages/fastqc/fastqc_0.11.x.patch
View file

31
var/spack/repos/builtin/packages/fastqc/fastqc_0.12.x.patch Normal file
View file

@ -0,0 +1,31 @@
--- fastqc.orig 2023-05-26 08:02:49.123718275 +0100
+++ fastqc 2023-05-26 08:12:19.980320240 +0100
@@ -38,13 +38,21 @@
$delimiter = ';';
}
-if ($ENV{CLASSPATH}) {
- $ENV{CLASSPATH} .= "$delimiter$RealBin$delimiter$RealBin/htsjdk.jar$delimiter$RealBin/jbzip2-0.9.jar$delimiter$RealBin/cisd-jhdf5.jar";
-}
-else {
- $ENV{CLASSPATH} = "$RealBin$delimiter$RealBin/htsjdk.jar$delimiter$RealBin/jbzip2-0.9.jar$delimiter$RealBin/cisd-jhdf5.jar";
-}
-
+# The lib dir is $RealBin/../lib
+# start with list of jars we need and prefix them with the lib dir
+# then stick CLASSPATH onto the front (empty or otherwise...)
+# then filter out anything that's empty (perhaps CLASSPATH...)
+# then join all the remainings bits with the delimiter.
+use File::Basename;
+use File::Spec::Functions;
+my $_lib = catfile(dirname($RealBin), 'lib');
+$ENV{CLASSPATH} =
+ join($delimiter,
+ grep {$_}
+ ($ENV{CLASSPATH},
+ $_lib,
+ map {"$_lib/$_"}
+ qw(htsjdk.jar jbzip2-0.9.jar cisd-jhdf5.jar)));
# We need to find the java interpreter. We'll start from the assumption that this
# is included in the path.

12
var/spack/repos/builtin/packages/fastqc/package.py
View file

@ -12,6 +12,7 @@ class Fastqc(Package):
homepage = "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
url = "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip"
version("0.12.1", sha256="5f4dba8780231a25a6b8e11ab2c238601920c9704caa5458d9de559575d58aa7")
version("0.11.9", sha256="15510a176ef798e40325b717cac556509fb218268cfdb9a35ea6776498321369")
version("0.11.7", sha256="59cf50876bbe5f363442eb989e43ae3eaab8d932c49e8cff2c1a1898dd721112")
version("0.11.5", sha256="dd7a5ad80ceed2588cf6d6ffe35e0f161c0d9977ed08355f5e4d9473282cbd66")
@ -20,7 +21,8 @@ class Fastqc(Package):
depends_on("java", type="run")
depends_on("perl") # for fastqc "script", any perl will do
patch("fastqc.patch", level=0)
patch("fastqc_0.12.x.patch", level=0, when="@0.12:")
patch("fastqc_0.11.x.patch", level=0, when="@:0.11.9")
def patch(self):
filter_file("/usr/bin/perl", self.spec["perl"].command.path, "fastqc", backup=False)
@ -29,8 +31,12 @@ def install(self, spec, prefix):
mkdir(prefix.bin)
mkdir(prefix.lib)
install("fastqc", prefix.bin)
for j in ["cisd-jhdf5.jar", "jbzip2-0.9.jar", "sam-1.103.jar"]:
install(j, prefix.lib)
install("cisd-jhdf5.jar", prefix.lib)
install("jbzip2-0.9.jar", prefix.lib)
if self.spec.satisfies("@:0.11.9"):
install("sam-1.103.jar", prefix.lib)
else:
install("htsjdk.jar", prefix.lib)
for d in ["Configuration", "net", "org", "Templates", "uk"]:
install_tree(d, join_path(prefix.lib, d))
chmod = which("chmod")