From cd2893640d7f4058d8a71a06a742c3847c3ab310 Mon Sep 17 00:00:00 2001
From: snehring <7978778+snehring@users.noreply.github.com>
Date: Fri, 21 Apr 2023 07:05:23 -0500
Subject: interproscan: add version 5.61-93.0, fix build issue (#37009)

---
 var/spack/repos/builtin/packages/interproscan/package.py   | 14 +++++++++-----
 .../repos/builtin/packages/interproscan/web-pom.patch      | 12 ++++++++++++
 2 files changed, 21 insertions(+), 5 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/interproscan/web-pom.patch

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/interproscan/package.py b/var/spack/repos/builtin/packages/interproscan/package.py
index 42073541e0..4bd5956f14 100644
--- a/var/spack/repos/builtin/packages/interproscan/package.py
+++ b/var/spack/repos/builtin/packages/interproscan/package.py
@@ -16,6 +16,7 @@ class Interproscan(Package):
     url = "https://github.com/ebi-pf-team/interproscan/archive/5.36-75.0.tar.gz"
     maintainers("snehring")
 
+    version("5.61-93.0", sha256="70aca3b14983733fe5119b6978cb707156d006d7f737aa60ce6c9addd6c288e4")
     version("5.56-89.0", sha256="75e6a8f86ca17356a2f77f75b07d6d8fb7b397c9575f6e9716b64983e490b230")
     version("5.38-76.0", sha256="cb191ff8eee275689b789167a57b368ea5c06bbcd36b4de23e8bbbbdc0fc7434")
     version("5.36-75.0", sha256="383d7431e47c985056c856ceb6d4dcf7ed2559a4a3d5c210c01ce3975875addb")
@@ -33,7 +34,7 @@ class Interproscan(Package):
     )
 
     depends_on("java@8.0:8.9", type=("build", "run"), when="@5:5.36-99.0")
-    depends_on("java@11.0:", type=("build", "run"), when="@5.37-76.0:")
+    depends_on("java@11", type=("build", "run"), when="@5.37-76.0:")
     depends_on("maven", type="build", when="@5:")
     depends_on("perl@5:", type=("build", "run"))
     depends_on("python@3:", when="@5:", type=("build", "run"))
@@ -48,19 +49,22 @@ class Interproscan(Package):
     patch("large-gid.patch", when="@5:")
     patch("non-interactive.patch", when="@:4.8")
     patch("ps_scan.patch", when="@:4.8")
+    patch("web-pom.patch", when="@5:")
 
     def install(self, spec, prefix):
         with working_dir("core"):
             if self.run_tests:
                 which("mvn")("verify")
             else:
-                which("mvn")("package", "-DskipTests")
+                which("mvn")("clean", "install", "-DskipTests")
+                with working_dir("jms-implementation"):
+                    which("mvn")("clean", "package", "-DskipTests")
 
-        install_tree(".", prefix)
+        target = join_path("core", "jms-implementation", "target", "interproscan-5-dist")
+        install_tree(target, 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)
+        symlink(join_path(prefix, "interproscan.sh"), join_path(prefix.bin, "interproscan.sh"))
 
     @when("@:4.8")
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/interproscan/web-pom.patch b/var/spack/repos/builtin/packages/interproscan/web-pom.patch
new file mode 100644
index 0000000000..41c69ab66a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/interproscan/web-pom.patch
@@ -0,0 +1,12 @@
+diff --git a/core/web/pom.xml b/core/web/pom.xml
+index d595aea0e..362dd0326 100644
+--- a/core/web/pom.xml
++++ b/core/web/pom.xml
+@@ -247,6 +247,7 @@
+                         <artifactId>maven-war-plugin</artifactId>
+                         <version>${mvn.war.version}</version>
+                         <configuration>
++			    <classifier>interpo-protein-page</classifier>
+                             <warName>interpro-protein-page</warName>
+                             <webResources>
+                                 <resource>
-- 
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