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interproscan: add version 5.61-93.0, fix build issue (#37009)

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snehring 2023-04-21 07:05:23 -05:00 committed by GitHub
parent b686974160
commit cd2893640d
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GPG Key ID: 4AEE18F83AFDEB23
2 changed files with 21 additions and 5 deletions
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14
var/spack/repos/builtin/packages/interproscan/package.py
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@ -16,6 +16,7 @@ class Interproscan(Package):
url = "https://github.com/ebi-pf-team/interproscan/archive/5.36-75.0.tar.gz" url = "https://github.com/ebi-pf-team/interproscan/archive/5.36-75.0.tar.gz"
maintainers("snehring") maintainers("snehring")
version("5.61-93.0", sha256="70aca3b14983733fe5119b6978cb707156d006d7f737aa60ce6c9addd6c288e4")
version("5.56-89.0", sha256="75e6a8f86ca17356a2f77f75b07d6d8fb7b397c9575f6e9716b64983e490b230") version("5.56-89.0", sha256="75e6a8f86ca17356a2f77f75b07d6d8fb7b397c9575f6e9716b64983e490b230")
version("5.38-76.0", sha256="cb191ff8eee275689b789167a57b368ea5c06bbcd36b4de23e8bbbbdc0fc7434") version("5.38-76.0", sha256="cb191ff8eee275689b789167a57b368ea5c06bbcd36b4de23e8bbbbdc0fc7434")
version("5.36-75.0", sha256="383d7431e47c985056c856ceb6d4dcf7ed2559a4a3d5c210c01ce3975875addb") 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@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("maven", type="build", when="@5:")
depends_on("perl@5:", type=("build", "run")) depends_on("perl@5:", type=("build", "run"))
depends_on("python@3:", when="@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("large-gid.patch", when="@5:")
patch("non-interactive.patch", when="@:4.8") patch("non-interactive.patch", when="@:4.8")
patch("ps_scan.patch", when="@:4.8") patch("ps_scan.patch", when="@:4.8")
patch("web-pom.patch", when="@5:")
def install(self, spec, prefix): def install(self, spec, prefix):
with working_dir("core"): with working_dir("core"):
if self.run_tests: if self.run_tests:
which("mvn")("verify") which("mvn")("verify")
else: 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 # link the main shell script into the PATH
ips_bin_suffix = "core/jms-implementation/target/interproscan-5-dist" symlink(join_path(prefix, "interproscan.sh"), join_path(prefix.bin, "interproscan.sh"))
symlink(join_path(prefix, ips_bin_suffix), prefix.bin)
@when("@:4.8") @when("@:4.8")
def install(self, spec, prefix): def install(self, spec, prefix):

12
var/spack/repos/builtin/packages/interproscan/web-pom.patch Normal file
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@ -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>