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Fri, 13 Nov 2020 04:43:15 -0800 (PST) From: zimoun In-Reply-To: References: Date: Fri, 13 Nov 2020 13:39:56 +0100 Message-ID: <86v9e9e8gz.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -1.0 (-) X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Scanner: ns3122888.ip-94-23-21.eu Authentication-Results: aspmx1.migadu.com; dkim=fail (headers rsa verify failed) header.d=gmail.com header.s=20161025 header.b=TiNpYE8Y; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Spam-Score: 0.09 X-TUID: 9cnIgReK5fYu Hi Roel, On Fri, 13 Nov 2020 at 12:01, Roel Janssen wrote: > With the following patches, I'd like to add samtools-1.9, htslib-1.9 > (samtools depends on that) to fix this problem with bedtools. Recently, investigating why the substitute of =E2=80=99python-pysam=E2=80= =99 was not available, I decided then to give a try at fixing the TODO: --8<---------------cut here---------------start------------->8--- (snippet '(begin ;; Drop bundled htslib. TODO: Also remove samtools ;; and bcftools. (delete-file-recursively "htslib") #t)))) --8<---------------cut here---------------end--------------->8--- And the bundled version is 1.9 (if I remember correctly), therefore because of: --8<---------------cut here---------------start------------->8--- (native-inputs `(("python-cython" ,python-cython) ;; Dependencies below are are for tests only. ("samtools" ,samtools) ("bcftools" ,bcftools) ("python-nose" ,python-nose))) --8<---------------cut here---------------end--------------->8--- some tests are unhappy. That=E2=80=99s said, these additions seem fine with me. :-) All the best, simon