From patchwork Wed Apr 28 14:05:09 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Roel Janssen X-Patchwork-Id: 28960 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 070EE27BC7D; Wed, 28 Apr 2021 15:06:24 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.9 required=5.0 tests=BAYES_00,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 6FEC727BC7C for ; Wed, 28 Apr 2021 15:06:23 +0100 (BST) Received: from localhost ([::1]:53600 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lbkpY-0001H0-TH for patchwork@mira.cbaines.net; Wed, 28 Apr 2021 10:06:21 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37928) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lbkpH-0001GD-0C for guix-patches@gnu.org; Wed, 28 Apr 2021 10:06:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:42193) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lbkpG-0004wV-NG for guix-patches@gnu.org; Wed, 28 Apr 2021 10:06:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lbkpG-0002wr-HL for guix-patches@gnu.org; Wed, 28 Apr 2021 10:06:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 28 Apr 2021 14:06:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47821 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Efraim Flashner Cc: 47821@debbugs.gnu.org Received: via spool by 47821-submit@debbugs.gnu.org id=B47821.161961872211280 (code B ref 47821); Wed, 28 Apr 2021 14:06:02 +0000 Received: (at 47821) by debbugs.gnu.org; 28 Apr 2021 14:05:22 +0000 Received: from localhost ([127.0.0.1]:53739 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lbkob-0002vr-Jx for submit@debbugs.gnu.org; Wed, 28 Apr 2021 10:05:22 -0400 Received: from eggs.gnu.org ([209.51.188.92]:57652) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lbkoZ-0002vc-CU for 47821@debbugs.gnu.org; Wed, 28 Apr 2021 10:05:20 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:44253) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lbkoS-0004Pq-Ht; Wed, 28 Apr 2021 10:05:14 -0400 Received: from 2001-1c02-0b18-2900-222e-248e-9586-e52d.cable.dynamic.v6.ziggo.nl ([2001:1c02:b18:2900:222e:248e:9586:e52d]:35472) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1lbkoR-00066q-SN; Wed, 28 Apr 2021 10:05:12 -0400 Message-ID: <63890b0475ea51a1215713195d929ff76b639630.camel@gnu.org> From: Roel Janssen Date: Wed, 28 Apr 2021 16:05:09 +0200 In-Reply-To: References: <9345d6a11fd99f1a8eefeb3664508938255e1287.camel@gnu.org> User-Agent: Evolution 3.40.0 (3.40.0-1.fc34) MIME-Version: 1.0 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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches On Tue, 2021-04-27 at 10:32 +0300, Efraim Flashner wrote: > On Fri, Apr 16, 2021 at 11:55:39AM +0200, Roel Janssen wrote: > > Hi Guix, > > > > The following patches update htslib, bcftools, samtools, and > > bedtools. > > I've succesfully built bedtools with the latest samtools instead of > > the > > 1.9 version. > > These look good and are ready for merging. Can you take a look at > python-pybedtools? There's a new version out which I hope builds with > the newer version of bedtools. > > Thanks. > I looked at python-pybedtools and came up with the following patch. The test phase is still not entirely happy because it ends with: --- ================ 497 passed, 3 xfailed, 426 warnings in 25.49s ================= Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/gnu/store/rz42ba0my9vrgbkjpkzr2drmnjk5ah50-python- 3.8.2/lib/python3.8/shutil.py", line 704, in rmtree orig_st = os.lstat(path) --- I attached the patch that I have that at least builds the newer version of python-pybedtools. I don't know how to further test it. Can I in the meantime already push the patches for updating htslib, bcftools, samtools and bedtools? Kind regards, Roel Janssen From 504b3d8ac6b7108b47091d93976e19df5757bf52 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 28 Apr 2021 16:00:38 +0200 Subject: [PATCH 5/5] gnu: Update python-pybedtools to 0.8.2. * gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.2; [disable-broken-tests]: Remove snippets for non-existing 'test_scripts.py'. --- gnu/packages/bioinformatics.scm | 23 ++++------------------- 1 file changed, 4 insertions(+), 19 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9b448dcd21..9dcae7f8b1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -815,13 +815,13 @@ intended to behave exactly the same as the original BWK awk.") (define-public python-pybedtools (package (name "python-pybedtools") - (version "0.8.1") + (version "0.8.2") (source (origin (method url-fetch) (uri (pypi-uri "pybedtools" version)) (sha256 (base32 - "14w5i40gi25clrr7h4wa2pcpnyipya8hrqi7nq77553zc5wf0df0")))) + "0wc7z8g8prgdx7n5chjva2fdq03wiwhqisjjxzkjg1j5k5ha7151")))) (build-system python-build-system) (arguments `(#:modules ((ice-9 ftw) @@ -834,13 +834,6 @@ intended to behave exactly the same as the original BWK awk.") (modify-phases %standard-phases (add-after 'unpack 'disable-broken-tests (lambda _ - (substitute* "pybedtools/test/test_scripts.py" - ;; This test freezes. - (("def test_intron_exon_reads") - "def _do_not_test_intron_exon_reads") - ;; This test fails in the Python 2 build. - (("def test_venn_mpl") - "def _do_not_test_venn_mpl")) (substitute* "pybedtools/test/test_helpers.py" ;; Requires internet access. (("def test_chromsizes") @@ -880,17 +873,9 @@ intended to behave exactly the same as the original BWK awk.") build-root-directory (find (cut string-prefix? "lib" <>) (scandir (string-append - build-root-directory))))) - (scripts (string-append - build-root-directory - (find (cut string-prefix? "scripts" <>) - (scandir build-root-directory))))) + build-root-directory)))))) (setenv "PYTHONPATH" - (string-append build ":" (getenv "PYTHONPATH"))) - ;; Executable scripts such as 'intron_exon_reads.py' must be - ;; available in the PATH. - (setenv "PATH" - (string-append scripts ":" (getenv "PATH")))) + (string-append build ":" (getenv "PYTHONPATH")))) ;; The tests need to be run from elsewhere... (mkdir-p "/tmp/test") (copy-recursively "pybedtools/test" "/tmp/test") -- 2.31.1