[bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools

[bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools

[Roel Janssen]

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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


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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(-)

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


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From 6a18bd05cdd181b19ab99f92f1ef87f1554c622d Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 16 Apr 2021 11:51:41 +0200
Subject: [PATCH 3/4] gnu: Update samtools to 1.12.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.12.
---
 gnu/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

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


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From f1513d7b43fa14e15d945c92fb9fa2c6451a46b9 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 16 Apr 2021 11:50:53 +0200
Subject: [PATCH 2/4] gnu: Update bcftools to 1.12.

* gnu/packages/bioinformatics.scm (bcftools): Update to 1.12.
---
 gnu/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

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


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From 45e578976cd0c77e60d2188385adcda51b23b92a Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 16 Apr 2021 11:49:49 +0200
Subject: [PATCH 1/4] gnu: htslib: Update to 1.12.

* gnu/packages/bioinformatics.scm (htslib): Update to 1.12.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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

[bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools

[Efraim Flashner]

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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.

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
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[bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools

[Roel Janssen]

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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


[-- Attachment #2: 0005-gnu-Update-python-pybedtools-to-0.8.2.patch --]
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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

[bug#47821] [PATCH] Update htslib, bcftools, samtools, bedtools

[Efraim Flashner]

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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.


-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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Confidentiality cannot be guaranteed on emails sent or received unencrypted

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bug#47821: [PATCH] Update htslib, bcftools, samtools, bedtools

[Roel Janssen]

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