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envelope-from=sl.lmysyibtgm3tgnjvg42dolbagezdknzxge2f2.a6nspo4xe2kk2@mawumag.com; helo=mail-200165.simplelogin.co X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Mailman-Approved-At: Thu, 23 May 2024 09:37:21 -0400 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-to: guix@mawumag.com X-ACL-Warn: , guix--- via Guix-patches X-Patchwork-Original-From: guix--- via Guix-patches via From: "ashish.is--- via Guix-patches\" via" Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches Updated kallisto to 0.50.1, it now supports more single-cell technologies (e.g. SPLiT-seq). I had to modify the 'do-not-use-bundled-htslib snippet to make one regex more selective---in this new version it the previous regex was mistakenly modifying parts of CMakeLists.txt other than the intended one. From 9bec1c5bf14b644ef7147b1bc66acaea6a903830 Mon Sep 17 00:00:00 2001 Message-ID: <9bec1c5bf14b644ef7147b1bc66acaea6a903830.1716457241.git.guix@mawumag.com> From: Marco Baggio Date: Thu, 23 May 2024 08:52:06 +0200 Subject: [PATCH] gnu: kallisto: Update to 0.50.1 Change-Id: I1b048be328f6d1d5034dfe29688a44f2af0b026a --- gnu/packages/bioinformatics.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b7e8e54de2..8dee300320 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14820,7 +14820,7 @@ (define-public segemehl (define-public kallisto (package (name "kallisto") - (version "0.48.0") + (version "0.50.1") (source (origin (method git-fetch) (uri (git-reference @@ -14829,7 +14829,7 @@ (define-public kallisto (file-name (git-file-name name version)) (sha256 (base32 - "0wx1ndmhndsd60952piaa925lk8bjr59d2yr1m2hcsqcb6cdjwpn")) + "0zfs79mv75599cf9d7d3c5a3s8idgz9qvl4qfzhvhbd87y3dv7p0")) (modules '((guix build utils))) (snippet '(delete-file-recursively "ext/htslib/")))) @@ -14841,16 +14841,16 @@ (define-public kallisto (add-after 'unpack 'do-not-use-bundled-htslib (lambda _ (substitute* "CMakeLists.txt" - (("^ExternalProject_Add" m) + (("^ExternalProject_Add\\(htslib[^\\)]*\\)" m) (string-append "if (NEVER)\n" m)) - (("^\\)") - (string-append ")\nendif(NEVER)")) (("include_directories\\(\\$\\{htslib_PREFIX.*" m) (string-append "# " m))) (substitute* "src/CMakeLists.txt" (("target_link_libraries\\(kallisto kallisto_core pthread \ -\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/../ext/htslib/libhts.a\\)") - "target_link_libraries(kallisto kallisto_core pthread hts)") +\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/../ext/htslib/libhts.a \ +\\$\\{install_dir\\}/build/src/libbifrost.a\\)") + "target_link_libraries(kallisto kallisto_core pthread hts \ +${install_dir}/build/src/libbifrost.a)") (("include_directories\\(\\.\\./ext/htslib\\)") ""))))))) (inputs (list hdf5 htslib-1.9 zlib)) base-commit: 3597c736588c45efde3c22d533ea8774c3fdd235 -- 2.41.0