From unknown Sat Sep 13 08:57:10 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#30658] [PATCH 0/4] Add FastQC Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 28 Feb 2018 22:32:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 30658 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 30658@debbugs.gnu.org Cc: Ricardo Wurmus X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.151985706732305 (code B ref -1); Wed, 28 Feb 2018 22:32:01 +0000 Received: (at submit) by debbugs.gnu.org; 28 Feb 2018 22:31:07 +0000 Received: from localhost ([127.0.0.1]:38020 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1erAFf-0008Oz-Ah for submit@debbugs.gnu.org; Wed, 28 Feb 2018 17:31:07 -0500 Received: from eggs.gnu.org ([208.118.235.92]:33952) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1erAFa-0008OS-Fw for submit@debbugs.gnu.org; Wed, 28 Feb 2018 17:31:04 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1erAFC-0006tw-JO for submit@debbugs.gnu.org; Wed, 28 Feb 2018 17:30:57 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,T_DKIM_INVALID autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:55234) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1erAFC-0006tJ-A2 for submit@debbugs.gnu.org; Wed, 28 Feb 2018 17:30:38 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:51990) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1erAEu-00070K-0T for guix-patches@gnu.org; Wed, 28 Feb 2018 17:30:37 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1erAEd-00062U-Pa for guix-patches@gnu.org; Wed, 28 Feb 2018 17:30:19 -0500 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21055) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1erAEd-0005u4-7O for guix-patches@gnu.org; Wed, 28 Feb 2018 17:30:03 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1519856083; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:To:Cc:Subject:Date:Message-Id; l=1070; bh=F6jsuTmDiBSuiaVCwrlC3yrT53j27mcsnK1b0XsUqCQ=; b=jAc6UV/zMF91BJ/IwOrCxag6f+XhFCeQDYc4nBFlnbrVZA1K00ZO5pGPkXWe3c6U bpT6CzIH2CD4gvPKmzIxlV3ZpV1Uj6gAXHfpI51kZp5pp9mLFJFBW43nsvl56APiviz eSVGgwjt76IMh7svKDtgvcsRp5SM8E2BeAi1qdt4= Received: from localhost (port-92-200-97-195.dynamic.qsc.de [92.200.97.195]) by mx.zohomail.com with SMTPS id 1519856083199695.6620493334095; Wed, 28 Feb 2018 14:14:43 -0800 (PST) From: Ricardo Wurmus Date: Wed, 28 Feb 2018 23:14:35 +0100 Message-Id: <20180228221435.26879-1-rekado@elephly.net> X-Mailer: git-send-email 2.16.2 X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.0 (----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -4.0 (----) Hi Guix, this patch adds fastqc, a very popular bioinformatics tool. This has been in my staging repo for a very long time because it is written in Java and bundled pre-built third-party jars. I finally managed to build the last few dependencies from source. These java-cisd-* packages were really not easy to build and you can tell by how complicated they are. Both java-cisd-base and java-cisd-jhdf5 include native libraries, which I'm building from the included C sources. The packages include tests, but unlike other Java packages these tests are in the form of an application that needs to be executed. Hence the extra build phase after "check" to actually run the tests. FastQC seems to work, but I haven't performed any comprehensive tests yet. Ricardo Wurmus (4): gnu: Add java-cisd-base. gnu: Add java-cisd-args4j. gnu: Add java-cisd-jhdf5. gnu: Add fastqc. gnu/packages/bioinformatics.scm | 79 ++++++++ gnu/packages/java.scm | 439 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 518 insertions(+) -- 2.16.2 From unknown Sat Sep 13 08:57:10 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#30658] [PATCH 3/4] gnu: Add java-cisd-jhdf5. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 28 Feb 2018 22:40:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 30658 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 30658@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 30658-submit@debbugs.gnu.org id=B30658.1519857559553 (code B ref 30658); Wed, 28 Feb 2018 22:40:02 +0000 Received: (at 30658) by debbugs.gnu.org; 28 Feb 2018 22:39:19 +0000 Received: from localhost ([127.0.0.1]:38027 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1erANb-00008o-5F for submit@debbugs.gnu.org; Wed, 28 Feb 2018 17:39:19 -0500 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21109) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1erANY-00008a-RO for 30658@debbugs.gnu.org; Wed, 28 Feb 2018 17:39:17 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1519857547; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:To:Cc:Subject:Date:Message-Id:In-Reply-To:References; l=7298; bh=VFeAmlnk/j0nw3JgcmqS+OimoQ3xExpS0kyhVEgY2wI=; b=g7iNvPQ3ZLa/rUbTqDA9+r/BRCkmHlJIJ091HKp3Ld+sjz1Efmj6WdCOKXcWv871 v28/scYopDq+JNOUlgqDmPxSno/ByEqbDyiLNp0oWDKp6BteB6uU0QxE+ho/O79IgOR GB6VCoiX8AUrvjckQsEzhUGp637rvTsIQC7dJ4R0= Received: from localhost (port-92-200-97-195.dynamic.qsc.de [92.200.97.195]) by mx.zohomail.com with SMTPS id 1519857547129473.09566505585224; Wed, 28 Feb 2018 14:39:07 -0800 (PST) From: Ricardo Wurmus Date: Wed, 28 Feb 2018 23:38:53 +0100 Message-Id: <20180228223854.31118-3-rekado@elephly.net> X-Mailer: git-send-email 2.16.2 In-Reply-To: <20180228223854.31118-1-rekado@elephly.net> References: <20180228223854.31118-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: -0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) * gnu/packages/java.scm (java-cisd-jhdf5): New variable. --- gnu/packages/java.scm | 176 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 176 insertions(+) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 7ad0c4126..298874f75 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -59,6 +59,7 @@ #:use-module (gnu packages image) #:use-module (gnu packages libffi) #:use-module (gnu packages linux) ;alsa + #:use-module (gnu packages maths) #:use-module (gnu packages web) #:use-module (gnu packages wget) #:use-module (gnu packages pkg-config) @@ -2347,6 +2348,181 @@ libraries from the SIS division at ETH Zurich like jHDF5.") (description "This package provides a parser for command line arguments.") (license license:asl2.0)))) +(define-public java-cisd-jhdf5 + (let ((revision 39162) + (base-version "14.12.6")) + (package + (name "java-cisd-jhdf5") + (version (string-append base-version "-" (number->string revision))) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "http://svnsis.ethz.ch/repos/cisd/" + "jhdf5/tags/release/" + (version-major+minor base-version) + ".x/" base-version "/jhdf5/")) + (revision revision))) + (file-name (string-append "java-cisd-jhdf5-" version "-checkout")) + (sha256 + (base32 + "13i17s2hn0q9drdqvp8csy7770p3hdbh9rp30ihln2ldkfawdmz0")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete included gradle jar + (delete-file-recursively "gradle/wrapper") + ;; Delete pre-built native libraries + (delete-file-recursively "libs") + #t)))) + (build-system ant-build-system) + (arguments + `(#:make-flags '("-file" "build/build.xml") + #:build-target "jar-all" + #:test-target "jar-test" + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + ;; Don't erase results from the build phase when building tests. + (add-after 'unpack 'separate-test-target-from-clean + (lambda _ + (substitute* "build/build.xml" + (("\"jar-test\" depends=\"clean, ") + "\"jar-test\" depends=\"")) + #t)) + (add-after 'unpack 'unpack-build-resources + (lambda* (#:key inputs #:allow-other-keys) + (copy-recursively (assoc-ref inputs "build-resources") + "../build_resources") + (delete-file-recursively "../build_resources/lib/") + (mkdir-p "../build_resources/lib") + ;; Remove dependency on classycle + (substitute* "../build_resources/ant/build-common.xml" + (("string revision)) + (("\\$\\{version.number\\}") ,base-version)) + #t)) + (add-after 'unpack-build-resources 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "../build_resources/ant/build-common.xml" + (("../libraries/testng/testng-jdk15.jar") + (string-append (assoc-ref inputs "java-testng") + "/share/java/java-testng.jar"))) + (substitute* "build/build.xml" + (("\\$\\{lib\\}/sis-base/sis-base.jar") + (string-append (assoc-ref inputs "java-cisd-base") + "/share/java/sis-base.jar")) + (("\\$\\{lib\\}/cisd-args4j/cisd-args4j.jar") + (string-append (assoc-ref inputs "java-cisd-args4j") + "/share/java/cisd-args4j.jar")) + (("\\$\\{lib\\}/commons-lang/commons-lang.jar") + (string-append (assoc-ref inputs "java-commons-lang") + "/share/java/commons-lang-" + ,(package-version java-commons-lang) ".jar")) + (("\\$\\{lib\\}/commons-io/commons-io.jar") + (string-append (assoc-ref inputs "java-commons-io") + "/share/java/commons-io-" + ,(package-version java-commons-io) + "-SNAPSHOT.jar")) + (("\\$\\{lib\\}/testng/testng-jdk15.jar") + (string-append (assoc-ref inputs "java-testng") + "/share/java/java-testng.jar")) + (("\\$\\{lib\\}/junit4/junit.jar") + (string-append (assoc-ref inputs "java-junit") + "/share/java/junit.jar")) + (("\\$\\{lib\\}/jmock/hamcrest/hamcrest-core.jar") + (string-append (assoc-ref inputs "java-hamcrest-core") + "/share/java/hamcrest-core.jar"))) + ;; Remove dependency on ch.rinn.restrictions + (with-directory-excursion "source/java/ch/systemsx/cisd/hdf5/" + (substitute* '("BitSetConversionUtils.java" + "HDF5Utils.java") + (("import ch.rinn.restrictions.Private;") "") + (("@Private") ""))) + (with-directory-excursion "sourceTest/java/ch/systemsx/cisd/hdf5/" + (substitute* '("BitSetConversionTest.java" + "h5ar/HDF5ArchiverTest.java") + (("import ch.rinn.restrictions.Friend;") "") + (("@Friend.*") "")) + ;; Remove leftovers from removing @Friend + (substitute* "h5ar/HDF5ArchiverTest.java" + (("\\{ HDF5Archiver.class, IdCache.class, LinkRecord.class \\}\\)") + ""))) + #t)) + (add-before 'configure 'build-native-library + (lambda* (#:key inputs #:allow-other-keys) + (let ((jdk (assoc-ref inputs "jdk")) + (hdf5 (assoc-ref inputs "hdf5")) + (dir ,(match (%current-system) + ("i686-linux" + "i386-Linux") + ((or "armhf-linux" "aarch64-linux") + "arm-Linux") + ((or "x86_64-linux") + "amd64-Linux") + (_ "unknown-Linux")))) + (with-directory-excursion "source/c" + (apply invoke `("gcc" "-shared" "-O3" + "-fPIC" + "-Wl,--exclude-libs,ALL" + ,@(find-files "jhdf5" "\\.c$") + ,@(find-files "hdf-java" "\\.c$") + ,(string-append "-I" hdf5 "/include") + ,(string-append "-I" jdk "/include") + ,(string-append "-I" jdk "/include/linux") + ,(string-append hdf5 "/lib/libhdf5.a") + "-o" "libjhdf5.so" "-lz"))) + (install-file "source/c/libjhdf5.so" + (string-append "libs/native/jhdf5/" dir)) + #t))) + ;; In the "check" phase we only build the test executable. + (add-after 'check 'run-tests + (lambda _ + (invoke "java" "-jar" "targets/dist/sis-jhdf5-test.jar") + (delete-file "targets/dist/sis-jhdf5-test.jar") + #t)) + (replace 'install + (install-jars "targets/dist"))))) + (inputs + `(("java-cisd-base" ,java-cisd-base) + ("java-cisd-args4j" ,java-cisd-args4j) + ("java-commons-lang" ,java-commons-lang) + ("java-commons-io" ,java-commons-io) + ("hdf5" ,hdf5) + ("zlib" ,zlib))) + (native-inputs + `(("jdk" ,icedtea-8) + ("java-testng" ,java-testng) + ("java-junit" ,java-junit) + ("java-jmock" ,java-jmock) + ("java-hamcrest-core" ,java-hamcrest-core) + ("build-resources" + ,(origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "http://svnsis.ethz.ch/repos/cisd/" + "jhdf5/tags/release/" + (version-major+minor base-version) + ".x/" base-version + "/build_resources/")) + (revision revision))) + (sha256 + (base32 + "0b6335gkm4x895rac6kfg9d3rpq0sy19ph4zpg2gyw6asfsisjhk")))))) + (home-page "https://wiki-bsse.ethz.ch/display/JHDF5/") + (synopsis "Java binding for HDF5") + (description "JHDF5 is a high-level API in Java for reading and writing +HDF5 files, building on the libraries provided by the HDF Group.") + ;; The C sources are under a non-copyleft license, which looks like a + ;; variant of the BSD licenses. The whole package is under the ASL2.0. + (license (list license:asl2.0 + (license:non-copyleft "file://source/c/COPYING")))))) + (define-public java-classpathx-servletapi (package (name "java-classpathx-servletapi") -- 2.16.2 From unknown Sat Sep 13 08:57:10 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#30658] [PATCH 4/4] gnu: Add fastqc. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 28 Feb 2018 22:40:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 30658 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 30658@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 30658-submit@debbugs.gnu.org id=B30658.1519857560559 (code B ref 30658); Wed, 28 Feb 2018 22:40:02 +0000 Received: (at 30658) by debbugs.gnu.org; 28 Feb 2018 22:39:20 +0000 Received: from localhost ([127.0.0.1]:38029 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1erANb-00008s-MT for submit@debbugs.gnu.org; Wed, 28 Feb 2018 17:39:20 -0500 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21113) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1erANZ-00008b-Ap for 30658@debbugs.gnu.org; Wed, 28 Feb 2018 17:39:18 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1519857551; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:To:Cc:Subject:Date:Message-Id:In-Reply-To:References; l=3336; bh=rC8+3vEZQdSQBmvxzX5QAwOmjWN6Rh7MV+rFLA5p8Jg=; b=bHQmLHhdaV8jYJV2BUJNiN3DMFlpHK3s4ypkvBrZ4FYE0kGhTriY59r0phcfoiMN nChoDAKj3srv8RXPaaeQiks7ssfiP+Hr4zuwb7R8MlF+0PcXL1HllStTZkrrkJcHLpJ GVW8nu9nLiFqO1XoiHZS7bLeuvwVfuMBkHGvBuzo= Received: from localhost (port-92-200-97-195.dynamic.qsc.de [92.200.97.195]) by mx.zohomail.com with SMTPS id 1519857551594353.08687383913764; Wed, 28 Feb 2018 14:39:11 -0800 (PST) From: Ricardo Wurmus Date: Wed, 28 Feb 2018 23:38:54 +0100 Message-Id: <20180228223854.31118-4-rekado@elephly.net> X-Mailer: git-send-email 2.16.2 In-Reply-To: <20180228223854.31118-1-rekado@elephly.net> References: <20180228223854.31118-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: -0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) * gnu/packages/bioinformatics.scm (fastqc): New variable. --- gnu/packages/bioinformatics.scm | 79 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 79 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c427a6d03..99fcf34f1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3211,6 +3211,85 @@ VCF.") ("jdk" ,icedtea-8 "jdk") ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop"))))))) +(define-public fastqc + (package + (name "fastqc") + (version "0.11.5") + (source + (origin + (method url-fetch) + (uri (string-append "http://www.bioinformatics.babraham.ac.uk/" + "projects/fastqc/fastqc_v" + version "_source.zip")) + (sha256 + (base32 + "18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; there are no tests + #:build-target "build" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build.xml" + (("jbzip2-0.9.jar") + (string-append (assoc-ref inputs "java-jbzip2") + "/share/java/jbzip2.jar")) + (("sam-1.103.jar") + (string-append (assoc-ref inputs "java-picard-1.113") + "/share/java/sam-1.112.jar")) + (("cisd-jhdf5.jar") + (string-append (assoc-ref inputs "java-cisd-jhdf5") + "/share/java/sis-jhdf5.jar"))) + #t)) + ;; There is no installation target + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (share (string-append out "/share/fastqc/")) + (exe (string-append share "/fastqc"))) + (for-each mkdir-p (list bin share)) + (copy-recursively "bin" share) + (substitute* exe + (("my \\$java_bin = 'java';") + (string-append "my $java_bin = '" + (assoc-ref inputs "java") + "/bin/java';"))) + (chmod exe #o555) + (symlink exe (string-append bin "/fastqc")) + #t)))))) + (inputs + `(("java" ,icedtea) + ("perl" ,perl) ; needed for the wrapper script + ("java-cisd-jhdf5" ,java-cisd-jhdf5) + ("java-picard-1.113" ,java-picard-1.113) + ("java-jbzip2" ,java-jbzip2))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/") + (synopsis "Quality control tool for high throughput sequence data") + (description + "FastQC aims to provide a simple way to do some quality control +checks on raw sequence data coming from high throughput sequencing +pipelines. It provides a modular set of analyses which you can use to +give a quick impression of whether your data has any problems of which +you should be aware before doing any further analysis. + +The main functions of FastQC are: + +@itemize +@item Import of data from BAM, SAM or FastQ files (any variant); +@item Providing a quick overview to tell you in which areas there may + be problems; +@item Summary graphs and tables to quickly assess your data; +@item Export of results to an HTML based permanent report; +@item Offline operation to allow automated generation of reports + without running the interactive application. +@end itemize\n") + (license license:gpl3+))) + (define-public htslib (package (name "htslib") -- 2.16.2 From unknown Sat Sep 13 08:57:10 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#30658] [PATCH 1/4] gnu: Add java-cisd-base. References: <20180228221435.26879-1-rekado@elephly.net> In-Reply-To: <20180228221435.26879-1-rekado@elephly.net> Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 28 Feb 2018 22:40:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 30658 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 30658@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 30658-submit@debbugs.gnu.org id=B30658.1519857564575 (code B ref 30658); Wed, 28 Feb 2018 22:40:06 +0000 Received: (at 30658) by debbugs.gnu.org; 28 Feb 2018 22:39:24 +0000 Received: from localhost ([127.0.0.1]:38032 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1erANg-00009D-3d for submit@debbugs.gnu.org; Wed, 28 Feb 2018 17:39:24 -0500 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21144) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1erANb-00008q-Pv for 30658@debbugs.gnu.org; Wed, 28 Feb 2018 17:39:20 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1519857538; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:To:Cc:Subject:Date:Message-Id; l=5843; bh=pxZu947OUCxgI08kG+ZZUnQsGU+uLp8qVm1zXslynaE=; b=YQodskQ1uIA+XrzcYLVNC2CwEA0iKPiuGiL3ZdaPVN4s3wgB5R3H7ehz5B5FsSm5 QdVNaLKs5ALpeQZCAVEXQhzdu+llC+QxSP4hBmCfWtKeQlt70tJcrZUMHjj8fQIlDMQ ez/hgc+gZ7o9d4dgWy0wNPQxpo7I9EO6ZyGTJpAM= Received: from localhost (port-92-200-97-195.dynamic.qsc.de [92.200.97.195]) by mx.zohomail.com with SMTPS id 151985753872619.45417695507342; Wed, 28 Feb 2018 14:38:58 -0800 (PST) From: Ricardo Wurmus Date: Wed, 28 Feb 2018 23:38:51 +0100 Message-Id: <20180228223854.31118-1-rekado@elephly.net> X-Mailer: git-send-email 2.16.2 X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: -0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) * gnu/packages/java.scm (java-cisd-base): New variable. --- gnu/packages/java.scm | 149 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 149 insertions(+) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 0f8c04e8b..1e2b30d8d 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -2084,6 +2084,155 @@ Main-Class: org.eclipse.jdt.internal.compiler.batch.Main\n" (native-inputs `(("unzip" ,unzip))))) +(define-public java-cisd-base + (let ((revision 38938) + (base-version "14.12.0")) + (package + (name "java-cisd-base") + (version (string-append base-version "-" (number->string revision))) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "http://svnsis.ethz.ch/repos/cisd/" + "base/tags/release/" + (version-major+minor base-version) + ".x/" base-version "/base/")) + (revision revision))) + (file-name (string-append "java-cisd-base-" version "-checkout")) + (sha256 + (base32 + "1i5adyf7nzclb0wydgwa1az04qliid8035vpahaandmkmigbnxiy")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete included gradle jar + (delete-file-recursively "gradle/wrapper") + ;; Delete pre-built native libraries + (delete-file-recursively "libs") + #t)))) + (build-system ant-build-system) + (arguments + `(#:make-flags '("-file" "build/build.xml") + #:test-target "jar-test" + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-build-resources + (lambda* (#:key inputs #:allow-other-keys) + (copy-recursively (assoc-ref inputs "build-resources") + "../build_resources") + #t)) + (add-after 'unpack-build-resources 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build/build.xml" + (("\\$\\{lib\\}/testng/testng-jdk15.jar") + (string-append (assoc-ref inputs "java-testng") + "/share/java/java-testng.jar")) + (("\\$\\{lib\\}/commons-lang/commons-lang.jar") + (string-append (assoc-ref inputs "java-commons-lang") + "/share/java/commons-lang-" + ,(package-version java-commons-lang) ".jar")) + (("\\$\\{lib\\}/commons-io/commons-io.jar") + (string-append (assoc-ref inputs "java-commons-io") + "/share/java/commons-io-" + ,(package-version java-commons-io) + "-SNAPSHOT.jar")) + ;; Remove dependency on svn + (("string revision)) + (("\\$\\{version.number\\}") ,base-version)) + ;; Remove dependency on classycle + (substitute* "../build_resources/ant/build-common.xml" + ((" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 01 Mar 2018 14:26:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 30658 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 30658@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 30658-submit@debbugs.gnu.org id=B30658.15199143292994 (code B ref 30658); Thu, 01 Mar 2018 14:26:02 +0000 Received: (at 30658) by debbugs.gnu.org; 1 Mar 2018 14:25:29 +0000 Received: from localhost ([127.0.0.1]:38351 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1erP9F-0000mE-7a for submit@debbugs.gnu.org; Thu, 01 Mar 2018 09:25:29 -0500 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21033) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1erP9D-0000m5-1E for 30658@debbugs.gnu.org; Thu, 01 Mar 2018 09:25:28 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1519857542; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:To:Cc:Subject:Date:Message-Id:In-Reply-To:References; l=4518; bh=NSqFgScyc8698bie1ORt8CXAMioxwv1DzbcC9PnWhZI=; b=WNQA4Nr8iWS/JdBd8A7yzoQH7Vnrtrxp8JOqVpQQ6UvU6VgB4ovBtzb4y/XOywLm Dv59iaidaVKhvMsnyzP5NZn2mJPk/qbQuM5YsUbfXL6DSMVpImrXO803BBuxnABKR0e oy0mqOL3EQFn8f8iUJNF1vxspHo0DDN0ZGvlAnQY= Received: from localhost (port-92-200-97-195.dynamic.qsc.de [92.200.97.195]) by mx.zohomail.com with SMTPS id 1519857542803107.03656925385985; Wed, 28 Feb 2018 14:39:02 -0800 (PST) From: Ricardo Wurmus Date: Wed, 28 Feb 2018 23:38:52 +0100 Message-Id: <20180228223854.31118-2-rekado@elephly.net> X-Mailer: git-send-email 2.16.2 In-Reply-To: <20180228223854.31118-1-rekado@elephly.net> References: <20180228223854.31118-1-rekado@elephly.net> X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-Spam-Score: -0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) * gnu/packages/java.scm (java-cisd-args4j): New variable. --- gnu/packages/java.scm | 114 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 114 insertions(+) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 1e2b30d8d..7ad0c4126 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -2233,6 +2233,120 @@ libraries from the SIS division at ETH Zurich like jHDF5.") (license (list license:asl2.0 (license:non-copyleft "file://source/c/COPYING")))))) +(define-public java-cisd-args4j + (let ((revision 39162) + (base-version "9.11.2")) + (package + (name "java-cisd-args4j") + (version (string-append base-version "-" (number->string revision))) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "http://svnsis.ethz.ch/repos/cisd/" + "args4j/tags/release/" + (version-major+minor base-version) + ".x/" base-version "/args4j/")) + (revision revision))) + (file-name (string-append "java-cisd-args4j-" version "-checkout")) + (sha256 + (base32 + "0hhqznjaivq7ips7mkwas78z42s6djsm20rrs7g1zd59rcsakxn2")))) + (build-system ant-build-system) + (arguments + `(#:make-flags '("-file" "build/build.xml") + #:tests? #f ; there are no tests + ;; There are weird build failures with JDK8, such as: "The type + ;; java.io.ObjectInputStream cannot be resolved. It is indirectly + ;; referenced from required .class files" + #:jdk ,icedtea-7 + #:modules ((guix build ant-build-system) + (guix build utils) + (guix build java-utils) + (sxml simple) + (sxml transform) + (sxml xpath)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-build-resources + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "../build_resources") + (invoke "tar" "xf" (assoc-ref inputs "build-resources") + "-C" "../build_resources" + "--strip-components=1") + (mkdir-p "../build_resources/lib") + #t)) + (add-after 'unpack-build-resources 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + ;; FIXME: There should be a more convenient abstraction for + ;; editing XML files. + (with-directory-excursion "../build_resources/ant/" + (chmod "build-common.xml" #o664) + (call-with-output-file "build-common.xml.new" + (lambda (port) + (sxml->xml + (pre-post-order + (with-input-from-file "build-common.xml" + (lambda _ (xml->sxml #:trim-whitespace? #t))) + `(;; Remove dependency on classycle and custom ant tasks + (taskdef . ,(lambda (tag . kids) + (let ((name ((sxpath '(name *text*)) kids))) + (if (or (member "build-info" name) + (member "dependency-checker" name) + (member "build-java-subprojects" name) + (member "project-classpath" name)) + '() ; skip + `(,tag ,@kids))))) + (typedef . ,(lambda (tag . kids) + (let ((name ((sxpath '(name *text*)) kids))) + (if (member "recursive-jar" name) + '() ; skip + `(,tag ,@kids))))) + (build-java-subprojects . ,(lambda _ '())) + ;; Ignore everything else + (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) + (*text* . ,(lambda (_ txt) txt)))) + port))) + (rename-file "build-common.xml.new" "build-common.xml")) + (substitute* "build/build.xml" + (("\\$\\{lib\\}/cisd-base/cisd-base.jar") + (string-append (assoc-ref inputs "java-cisd-base") + "/share/java/sis-base.jar")) + ;; Remove dependency on svn + (("string revision)) + (("\\$\\{version.number\\}") ,base-version) + ;; Don't use custom ant tasks. + (("recursive-jar") "jar") + ((") id 1euQM2-0003Dk-GG for submit@debbugs.gnu.org; Fri, 09 Mar 2018 17:19:10 -0500 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21108) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1euQM0-0003DZ-J0 for control@debbugs.gnu.org; Fri, 09 Mar 2018 17:19:09 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1520633939; s=zoho; d=elephly.net; i=rekado@elephly.net; h=Date:To:From:Subject; l=31; bh=Y2AAO+WJ2k6Lu1gPPhpmVHK7gy37Ny9bXZLhxymWwyg=; b=aesl7kZ0IvGyJaSSMdmDcXAj+5/i1ohC+Nz9f4nAudZ9GnMhQ/19zKVdEBmZ0vjp sfGx7r5imdc9YSCTWPqMWC4YHfA18j5SwmDHlucqMEViaHV6oG4INTvOpgDJeMfhU0+ ClQy9hR7W4t6KL1Gk6nCQom5qfLFb/M7YGQtMtwE= Received: from localhost (port-92-200-43-38.dynamic.qsc.de [92.200.43.38]) by mx.zohomail.com with SMTPS id 1520633939734661.0132934271126; Fri, 9 Mar 2018 14:18:59 -0800 (PST) Date: Fri, 09 Mar 2018 23:18:57 +0100 To: control@debbugs.gnu.org From: Ricardo Wurmus Subject: control message for bug #30658 X-ZohoMailClient: External X-Spam-Score: 0.1 (/) X-Debbugs-Envelope-To: control X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" Message-Id: X-Spam-Score: -0.0 (/) tags 30658 fixed close 30658