[PATCH] Update htslib, bcftools, samtools, bedtools

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2 participants

Efraim Flashner
Roel Janssen

Owner: unassigned

Submitted by: Roel Janssen

Severity: normal

Roel Janssen wrote on 16 Apr 2021 11:55

Recipients:(address . guix-patches@gnu.org)

Message-ID:9345d6a11fd99f1a8eefeb3664508938255e1287.camel@gnu.org

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.

Kind regards,

Roel Janssen

From 4549f622042cb8c04165d85ff922d129f7c10553 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 16 Apr 2021 11:52:16 +0200
Subject: [PATCH 4/4] gnu: Update bedtools to 2.30.0.

* gnu/packages/bioinformatics.scm (bedtools): Update to 2.30.0,
  [inputs]: Use latest samtools.
---
 gnu/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

Toggle diff (33 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2a20971089..94bf917df5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -453,7 +453,7 @@ computational cluster.")
 (define-public bedtools
   (package
     (name "bedtools")
-    (version "2.29.2")
+    (version "2.30.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/arq5x/bedtools2/releases/"
@@ -461,7 +461,7 @@ computational cluster.")
                                   "bedtools-" version ".tar.gz"))
               (sha256
                (base32
-                "0m3hk6548846w83a9s5drsczvy67n2azx41kj71n03klb2gbzwg3"))))
+                "1f2hh79l7dn147c2xyfgf5wfjvlqfw32kjfnnh2n1qy6rpzx2fik"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"
@@ -473,7 +473,7 @@ computational cluster.")
     (native-inputs
      `(("python" ,python-wrapper)))
     (inputs
-     `(("samtools" ,samtools-1.9)
+     `(("samtools" ,samtools)
        ("zlib" ,zlib)))
     (home-page "https://github.com/arq5x/bedtools2")
     (synopsis "Tools for genome analysis and arithmetic")
-- 
2.30.2

From 6a18bd05cdd181b19ab99f92f1ef87f1554c622d Mon Sep 17 00:00:00 2001

* gnu/packages/bioinformatics.scm (samtools): Update to 1.12.

---

gnu/packages/bioinformatics.scm | 6 +++---

1 file changed, 3 insertions(+), 3 deletions(-)

Toggle diff (29 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a7cffdf83c..2a20971089 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5901,7 +5901,7 @@ to the user's query of interest.")
 (define-public samtools
   (package
     (name "samtools")
-    (version "1.11")
+    (version "1.12")
     (source
      (origin
        (method url-fetch)
@@ -5910,11 +5910,11 @@ to the user's query of interest.")
                        version "/samtools-" version ".tar.bz2"))
        (sha256
         (base32
-         "1dp5wknak4arnw5ghhif9mmljlfnw5bgm91wib7z0j8wdjywx0z2"))
+         "1jrdj2idpma5ja9cg0rr73b565vdbr9wyy6zig54bidicc2pg8vd"))
        (modules '((guix build utils)))
        (snippet '(begin
                    ;; Delete bundled htslib.
-                   (delete-file-recursively "htslib-1.11")
+                   (delete-file-recursively "htslib-1.12")
                    #t))))
     (build-system gnu-build-system)
     (arguments
-- 
2.30.2

From f1513d7b43fa14e15d945c92fb9fa2c6451a46b9 Mon Sep 17 00:00:00 2001

* gnu/packages/bioinformatics.scm (bcftools): Update to 1.12.

---

gnu/packages/bioinformatics.scm | 6 +++---

1 file changed, 3 insertions(+), 3 deletions(-)

Toggle diff (29 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e385e07cea..a7cffdf83c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -327,7 +327,7 @@ BAM files.")
 (define-public bcftools
   (package
     (name "bcftools")
-    (version "1.11")
+    (version "1.12")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/samtools/bcftools/"
@@ -335,11 +335,11 @@ BAM files.")
                                   version "/bcftools-" version ".tar.bz2"))
               (sha256
                (base32
-                "0r508mp15pqzf8r1269kb4v5naw9zsvbwd3cz8s1yj7carsf9viw"))
+                "1x94l1hy2pi3lbz0sxlbw0g6q5z5apcrhrlcwda94ns9n4r6a3ks"))
               (modules '((guix build utils)))
               (snippet '(begin
                           ;; Delete bundled htslib.
-                          (delete-file-recursively "htslib-1.11")
+                          (delete-file-recursively "htslib-1.12")
                           #t))))
     (build-system gnu-build-system)
     (arguments
-- 
2.30.2

From 45e578976cd0c77e60d2188385adcda51b23b92a Mon Sep 17 00:00:00 2001

* gnu/packages/bioinformatics.scm (htslib): Update to 1.12.

---

gnu/packages/bioinformatics.scm | 4 ++--

1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (24 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 41ef4cd513..e385e07cea 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4476,7 +4476,7 @@ performance.")
 (define-public htslib
   (package
     (name "htslib")
-    (version "1.11")
+    (version "1.12")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -4484,7 +4484,7 @@ performance.")
                     version "/htslib-" version ".tar.bz2"))
               (sha256
                (base32
-                "1mrq4mihzx37yqhj3sfz6da6mw49niia808bzsw2gkkgmadxvyng"))))
+                "1jplnvizgr0fyyvvmkfmnsywrrpqhid3760vw15bllz98qdi9012"))))
     (build-system gnu-build-system)
     ;; Let htslib translate "gs://" and "s3://" to regular https links with
     ;; "--enable-gcs" and "--enable-s3". For these options to work, we also
-- 
2.30.2

Efraim Flashner wrote on 27 Apr 2021 09:32

Recipients:(name . Roel Janssen)(address . roel@gnu.org)(address . 47821@debbugs.gnu.org)

Message-ID:YIe9/Q8gLrucnOZc@3900XT

On Fri, Apr 16, 2021 at 11:55:39AM +0200, Roel Janssen wrote:

Toggle quote (6 lines)

> 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.

Efraim Flashner <efraim@flashner.co.il> ????? ?????

GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351

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Roel Janssen wrote on 28 Apr 2021 16:05

Recipients:(name . Efraim Flashner)(address . efraim@flashner.co.il)(address . 47821@debbugs.gnu.org)

Message-ID:63890b0475ea51a1215713195d929ff76b639630.camel@gnu.org

On Tue, 2021-04-27 at 10:32 +0300, Efraim Flashner wrote:

Toggle quote (16 lines)> 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 <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(-)

Toggle diff (56 lines)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

Efraim Flashner wrote on 29 Apr 2021 08:43

Recipients:(name . Roel Janssen)(address . roel@gnu.org)(address . 47821@debbugs.gnu.org)

Message-ID:YIpVlwfoX5gK7Uez@3900XT

On Wed, Apr 28, 2021 at 04:05:09PM +0200, Roel Janssen wrote:

Toggle quote (37 lines)> 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.

Efraim Flashner <efraim@flashner.co.il> ????? ?????

GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351

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Roel Janssen wrote on 29 Apr 2021 12:21

Recipients:(name . Efraim Flashner)(address . efraim@flashner.co.il)(address . 47821-done@debbugs.gnu.org)

Message-ID:42f9d1f0-88d6-beb7-81c1-ef1b0e501ff2@gnu.org

On 4/29/21 8:43 AM, Efraim Flashner wrote:

Toggle quote (36 lines)> 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

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