| Message ID | 63890b0475ea51a1215713195d929ff76b639630.camel@gnu.org |
|---|---|
| State | Accepted |
| Headers | show |
| Series | [bug#47821] Update htslib, bcftools, samtools, bedtools | expand |
| Context | Check | Description |
|---|---|---|
| cbaines/comparison | success | View comparision |
| cbaines/git branch | success | View Git branch |
| cbaines/applying patch | fail | View Laminar job |
| cbaines/issue | success | View issue |
On Wed, Apr 28, 2021 at 04:05:09PM +0200, Roel Janssen wrote: > 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? > Yeah, those patches LGTM.
On 4/29/21 8:43 AM, Efraim Flashner wrote: > On Wed, Apr 28, 2021 at 04:05:09PM +0200, Roel Janssen wrote: >> 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? >> > Yeah, those patches LGTM. Thanks. I pushed these. For python-pybedtools, I think a little bit more testing is required. I can take a look at it in the second week of May, so hopefully someone beats me to it. :) Kind regards, Roel Janssen
From 504b3d8ac6b7108b47091d93976e19df5757bf52 Mon Sep 17 00:00:00 2001 From: Roel Janssen <roel@gnu.org> 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