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

* 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>

3 files changed, 40 insertions, 3 deletions

diff --git a/var/spack/repos/builtin/packages/fastqc/fastqc.patch b/var/spack/repos/builtin/packages/fastqc/fastqc_0.11.x.patch
index a0a1155905..a0a1155905 100644
--- a/var/spack/repos/builtin/packages/fastqc/fastqc.patch
+++ b/var/spack/repos/builtin/packages/fastqc/fastqc_0.11.x.patch
diff --git a/var/spack/repos/builtin/packages/fastqc/fastqc_0.12.x.patch b/var/spack/repos/builtin/packages/fastqc/fastqc_0.12.x.patch
new file mode 100644
index 0000000000..1e4fd23c9c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fastqc/fastqc_0.12.x.patch
@@ -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.
diff --git a/var/spack/repos/builtin/packages/fastqc/package.py b/var/spack/repos/builtin/packages/fastqc/package.py
index 247c00dab7..b2a1cf7b64 100644
--- a/var/spack/repos/builtin/packages/fastqc/package.py
+++ b/var/spack/repos/builtin/packages/fastqc/package.py
@@ -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 @@ class Fastqc(Package):
         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")