GNU bug report logs -
#47930
[PATCH] gnu: Add pbgzip.
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Reported by: Roel Janssen <roel <at> gnu.org>
Date: Wed, 21 Apr 2021 12:28:02 UTC
Severity: normal
Tags: patch
Done: Roel Janssen <roel <at> gnu.org>
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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
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Hi Guix,
Here's a patch to add pbgzip. Lint complains that there is no release
on the Github page, but there's nothing I can do about it.
Kind regards,
Roel Janssen
[0001-gnu-Add-pbgzip.patch (text/x-patch, attachment)]
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Message #8 received at 47930 <at> debbugs.gnu.org (full text, mbox):
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On Wed, Apr 21 2021, Roel Janssen wrote:
> * gnu/packages/bioinformatics.scm (pbgzip): New variable.
>
> [...]
>
> +(define-public pbgzip
> + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974"))
> + (package
> + (name "pbgzip")
> + (version (string-take commit 7))
I think using (git-version VERSION REVISION COMMIT) is preferred.
Something like (git-version "0.0.0" "0" commit).
> + (source (origin
> + (method git-fetch)
> + (uri (git-reference
> + (url "https://github.com/nh13/pbgzip")
> + (commit commit)))
> + (file-name (string-append name "-" version))
Use (git-file-name name version).
> + (sha256
> + (base32
> + "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd"))))
> + (build-system gnu-build-system)
> + (arguments
> + `(#:phases
> + (modify-phases %standard-phases
> + (add-after 'unpack 'autogen
> + (lambda _
> + (zero? (system* "sh" "autogen.sh")))))))
IIRC, phases don’t have to return #t, so you could remove ‘zero?’.
Builds fine, but I haven’t tested it.
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Message #11 received at 47930 <at> debbugs.gnu.org (full text, mbox):
On Wed, Apr 21 2021, Roel Janssen wrote:
> * gnu/packages/bioinformatics.scm (pbgzip): New variable.
>
> [...]
>
> +(define-public pbgzip
> + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974"))
> + (package
> + (name "pbgzip")
> + (version (string-take commit 7))
I think using (git-version VERSION REVISION COMMIT) is preferred.
Something like (git-version "0.0.0" "0" commit).
> + (source (origin
> + (method git-fetch)
> + (uri (git-reference
> + (url "https://github.com/nh13/pbgzip")
> + (commit commit)))
> + (file-name (string-append name "-" version))
Use (git-file-name name version).
> + (sha256
> + (base32
> + "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd"))))
> + (build-system gnu-build-system)
> + (arguments
> + `(#:phases
> + (modify-phases %standard-phases
> + (add-after 'unpack 'autogen
> + (lambda _
> + (zero? (system* "sh" "autogen.sh")))))))
IIRC, phases don’t have to return #t, so you could remove ‘zero?’.
Builds fine, but I haven’t tested it.
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Message #14 received at 47930 <at> debbugs.gnu.org (full text, mbox):
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Xinglu Chen schreef op wo 21-04-2021 om 23:45 [+0200]:
> On Wed, Apr 21 2021, Roel Janssen wrote:
>
> > [...]
> > + (arguments
> > + `(#:phases
> > + (modify-phases %standard-phases
> > + (add-after 'unpack 'autogen
> > + (lambda _
> > + (zero? (system* "sh" "autogen.sh")))))))
>
> IIRC, phases don’t have to return #t, so you could remove ‘zero?’.
Try running (system* "does-not-exist"). It will fail by returning
something non-zero. If I recall how to call "invoke" correctly,
I would recommend (invoke "sh" "autogen.sh") here. "invoke" raises
an exception when the command fails, instead of returning something.
Greetings,
Maxime.
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Message #17 received at 47930 <at> debbugs.gnu.org (full text, mbox):
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On Thu, Apr 22, 2021 at 06:40:46PM +0200, Maxime Devos wrote:
> Xinglu Chen schreef op wo 21-04-2021 om 23:45 [+0200]:
> > On Wed, Apr 21 2021, Roel Janssen wrote:
> >
> > > [...]
> > > + (arguments
> > > + `(#:phases
> > > + (modify-phases %standard-phases
> > > + (add-after 'unpack 'autogen
> > > + (lambda _
> > > + (zero? (system* "sh" "autogen.sh")))))))
> >
> > IIRC, phases don’t have to return #t, so you could remove ‘zero?’.
>
> Try running (system* "does-not-exist"). It will fail by returning
> something non-zero. If I recall how to call "invoke" correctly,
> I would recommend (invoke "sh" "autogen.sh") here. "invoke" raises
> an exception when the command fails, instead of returning something.
While we're at it, can this phase replace 'bootstrap? It seems to me we
shouldn't need both phases.
--
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Message #20 received at 47930 <at> debbugs.gnu.org (full text, mbox):
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On 4/29/21 9:29 AM, Efraim Flashner wrote:
> On Thu, Apr 22, 2021 at 06:40:46PM +0200, Maxime Devos wrote:
>> Xinglu Chen schreef op wo 21-04-2021 om 23:45 [+0200]:
>>> On Wed, Apr 21 2021, Roel Janssen wrote:
>>>
>>>> [...]
>>>> + (arguments
>>>> + `(#:phases
>>>> + (modify-phases %standard-phases
>>>> + (add-after 'unpack 'autogen
>>>> + (lambda _
>>>> + (zero? (system* "sh" "autogen.sh")))))))
>>> IIRC, phases don’t have to return #t, so you could remove ‘zero?’.
>> Try running (system* "does-not-exist"). It will fail by returning
>> something non-zero. If I recall how to call "invoke" correctly,
>> I would recommend (invoke "sh" "autogen.sh") here. "invoke" raises
>> an exception when the command fails, instead of returning something.
> While we're at it, can this phase replace 'bootstrap? It seems to me we
> shouldn't need both phases.
This indeed seems to be the best thing to do. I attached a new patch.
I had to leave autoconf and automake in the native-inputs because
otherwise the command "aclocal" and "autom4te" couldn't be found.
Thanks all for the feedback! I hope this new patch is fine.
Kind regards,
Roel Janssen
[0001-gnu-Add-pbgzip.patch (text/x-patch, attachment)]
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Message #23 received at 47930 <at> debbugs.gnu.org (full text, mbox):
On Thu, Apr 29 2021, Roel Janssen wrote:
> +(define-public pbgzip
> + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974"))
> + (package
> + (name "pbgzip")
> + (version (string-take commit 7))
Maybe you missed my previous suggestions?
https://issues.guix.gnu.org/47930#2
> + (source (origin
> + (method git-fetch)
> + (uri (git-reference
> + (url "https://github.com/nh13/pbgzip")
> + (commit commit)))
> + (file-name (string-append name "-" version))
> + (sha256
> + (base32
> + "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd"))))
> + (build-system gnu-build-system)
> + (native-inputs
> + `(("autoconf" ,autoconf)
> + ("automake" ,automake)))
> + (inputs
> + `(("zlib" ,zlib)))
> + (home-page "https://github.com/nh13/pbgzip")
> + (synopsis "Parallel Block GZIP")
> + (description "This package implements parallel block gzip. For many
> +formats, in particular genomics data formats, data are compressed in
> +fixed-length blocks such that they can be easily indexed based on a (genomic)
> +coordinate order, since typically each block is sorted according to this order.
> +This allows for each block to be individually compressed (deflated), or more
> +importantly, decompressed (inflated), with the latter enabling random retrieval
> +of data in large files (gigabytes to terabytes). @code{pbgzip} is not limited
> +to any particular format, but certain features are tailored to genomics data
> +formats when enabled. Parallel decompression is somewhat faster, but truly the
^^^^^^^^^^^^^
> +speedup comes during compression.")
^^^^^^^
“but the true speedup” instead?
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Message #26 received at 47930 <at> debbugs.gnu.org (full text, mbox):
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On Fri, 2021-04-30 at 10:30 +0200, Xinglu Chen wrote:
> On Thu, Apr 29 2021, Roel Janssen wrote:
>
> > +(define-public pbgzip
> > + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974"))
> > + (package
> > + (name "pbgzip")
> > + (version (string-take commit 7))
>
> Maybe you missed my previous suggestions?
>
> https://issues.guix.gnu.org/47930#2
>
I'm sorry, I forgot to adapt.
>
> > + (source (origin
> > + (method git-fetch)
> > + (uri (git-reference
> > + (url "https://github.com/nh13/pbgzip")
> > + (commit commit)))
> > + (file-name (string-append name "-" version))
> > + (sha256
> > + (base32
> > +
> > "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd"))))
> > + (build-system gnu-build-system)
> > + (native-inputs
> > + `(("autoconf" ,autoconf)
> > + ("automake" ,automake)))
> > + (inputs
> > + `(("zlib" ,zlib)))
> > + (home-page "https://github.com/nh13/pbgzip")
> > + (synopsis "Parallel Block GZIP")
> > + (description "This package implements parallel block gzip.
> > For many
> > +formats, in particular genomics data formats, data are compressed
> > in
> > +fixed-length blocks such that they can be easily indexed based on
> > a (genomic)
> > +coordinate order, since typically each block is sorted according
> > to this order.
> > +This allows for each block to be individually compressed
> > (deflated), or more
> > +importantly, decompressed (inflated), with the latter enabling
> > random retrieval
> > +of data in large files (gigabytes to terabytes). @code{pbgzip} is
> > not limited
> > +to any particular format, but certain features are tailored to
> > genomics data
> > +formats when enabled. Parallel decompression is somewhat faster,
> > but truly the
>
> ^^^^^^^^^^^^^
> > +speedup comes during compression.")
> ^^^^^^^
>
> “but the true speedup” instead?
Sure. I usually don't change descriptions as given by the creators of
the software, but I applied your suggestion.
Thank you for the elaborate suggestions!
I attached another version of the patch, which I hope is fine now. :)
Kind regards,
Roel Janssen
[0001-gnu-Add-pbgzip.patch (text/x-patch, attachment)]
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Message #29 received at 47930 <at> debbugs.gnu.org (full text, mbox):
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On Fri, Apr 30, 2021 at 01:48:48PM +0200, Roel Janssen wrote:
> On Fri, 2021-04-30 at 10:30 +0200, Xinglu Chen wrote:
> > On Thu, Apr 29 2021, Roel Janssen wrote:
> >
> > > +(define-public pbgzip
> > > + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974"))
> > > + (package
> > > + (name "pbgzip")
> > > + (version (string-take commit 7))
> >
> > Maybe you missed my previous suggestions?
> >
> > https://issues.guix.gnu.org/47930#2
> >
>
> I'm sorry, I forgot to adapt.
> >
> > > + (source (origin
> > > + (method git-fetch)
> > > + (uri (git-reference
> > > + (url "https://github.com/nh13/pbgzip")
> > > + (commit commit)))
> > > + (file-name (string-append name "-" version))
> > > + (sha256
> > > + (base32
> > > +
> > > "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd"))))
> > > + (build-system gnu-build-system)
> > > + (native-inputs
> > > + `(("autoconf" ,autoconf)
> > > + ("automake" ,automake)))
> > > + (inputs
> > > + `(("zlib" ,zlib)))
> > > + (home-page "https://github.com/nh13/pbgzip")
> > > + (synopsis "Parallel Block GZIP")
> > > + (description "This package implements parallel block gzip.
> > > For many
> > > +formats, in particular genomics data formats, data are compressed
> > > in
> > > +fixed-length blocks such that they can be easily indexed based on
> > > a (genomic)
> > > +coordinate order, since typically each block is sorted according
> > > to this order.
> > > +This allows for each block to be individually compressed
> > > (deflated), or more
> > > +importantly, decompressed (inflated), with the latter enabling
> > > random retrieval
> > > +of data in large files (gigabytes to terabytes). @code{pbgzip} is
> > > not limited
> > > +to any particular format, but certain features are tailored to
> > > genomics data
> > > +formats when enabled. Parallel decompression is somewhat faster,
> > > but truly the
> >
> > ^^^^^^^^^^^^^
> > > +speedup comes during compression.")
> > ^^^^^^^
> >
> > “but the true speedup” instead?
>
> Sure. I usually don't change descriptions as given by the creators of
> the software, but I applied your suggestion.
>
> Thank you for the elaborate suggestions!
>
> I attached another version of the patch, which I hope is fine now. :)
>
> Kind regards,
> Roel Janssen
>
>
> From 1af29f66980ba19740e05a27135f141e23b7fd3f Mon Sep 17 00:00:00 2001
> From: Roel Janssen <roel <at> gnu.org>
> Date: Fri, 30 Apr 2021 13:47:43 +0200
> Subject: [PATCH] gnu: Add pbgzip.
>
> * gnu/packages/bioinformatics.scm (pbgzip): New variable.
> ---
> gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++-
> 1 file changed, 35 insertions(+), 1 deletion(-)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 83ebfc2d8f..cd2dae05d5 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -3,7 +3,7 @@
> ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben <at> gmail.com>
> ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix <at> thebird.nl>
> ;;; Copyright © 2015 Andreas Enge <andreas <at> enge.fr>
> -;;; Copyright © 2016, 2020 Roel Janssen <roel <at> gnu.org>
> +;;; Copyright © 2016, 2020, 2021 Roel Janssen <roel <at> gnu.org>
> ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim <at> flashner.co.il>
> ;;; Copyright © 2016, 2020 Marius Bakke <mbakke <at> fastmail.com>
> ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo <at> gmail.com>
> @@ -571,6 +571,40 @@ input and output BAMs must adhere to the PacBio BAM format specification.
> Non-PacBio BAMs will cause exceptions to be thrown.")
> (license license:bsd-3)))
>
> +(define-public pbgzip
> + (let ((commit "2b09f97b5f20b6d83c63a5c6b408d152e3982974"))
> + (package
> + (name "pbgzip")
> + (version (git-version "0.0.0" "0" commit))
> + (source (origin
> + (method git-fetch)
> + (uri (git-reference
> + (url "https://github.com/nh13/pbgzip")
> + (commit commit)))
> + (file-name (git-file-name name version))
> + (sha256
> + (base32
> + "1mlmq0v96irbz71bgw5zcc43g1x32zwnxx21a5p1f1ch4cikw1yd"))))
> + (build-system gnu-build-system)
> + (native-inputs
> + `(("autoconf" ,autoconf)
> + ("automake" ,automake)))
> + (inputs
> + `(("zlib" ,zlib)))
> + (home-page "https://github.com/nh13/pbgzip")
> + (synopsis "Parallel Block GZIP")
> + (description "This package implements parallel block gzip. For many
> +formats, in particular genomics data formats, data are compressed in
I wasn't sure about 'data are' vs 'data is' but I think data here is
plural, so 'data are' should be right.
> +fixed-length blocks such that they can be easily indexed based on a (genomic)
> +coordinate order, since typically each block is sorted according to this order.
> +This allows for each block to be individually compressed (deflated), or more
> +importantly, decompressed (inflated), with the latter enabling random retrieval
> +of data in large files (gigabytes to terabytes). @code{pbgzip} is not limited
> +to any particular format, but certain features are tailored to genomics data
> +formats when enabled. Parallel decompression is somewhat faster, but the true
> +speedup comes during compression.")
> + (license license:expat))))
> +
> (define-public blasr-libcpp
> (package
> (name "blasr-libcpp")
> --
> 2.31.1
>
Looks good to me!
--
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(Fri, 30 Apr 2021 16:49:01 GMT)
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Message #34 received at 47930-done <at> debbugs.gnu.org (full text, mbox):
On Fri, 2021-04-30 at 14:53 +0300, Efraim Flashner wrote:
>
>
> > From 1af29f66980ba19740e05a27135f141e23b7fd3f Mon Sep 17 00:00:00
> > 2001
> > From: Roel Janssen <roel <at> gnu.org>
> > Date: Fri, 30 Apr 2021 13:47:43 +0200
> > Subject: [PATCH] gnu: Add pbgzip.
> >
> > ...
> > + (synopsis "Parallel Block GZIP")
> > + (description "This package implements parallel block gzip.
> > For many
> > +formats, in particular genomics data formats, data are compressed
> > in
>
> I wasn't sure about 'data are' vs 'data is' but I think data here is
> plural, so 'data are' should be right.
>
> > +fixed-length blocks such that they can be easily indexed based on
> > a (genomic)
> > +coordinate order, since typically each block is sorted according
> > to this order.
> > +This allows for each block to be individually compressed
> > (deflated), or more
> > +importantly, decompressed (inflated), with the latter enabling
> > random retrieval
> > +of data in large files (gigabytes to terabytes). @code{pbgzip} is
> > not limited
> > +to any particular format, but certain features are tailored to
> > genomics data
> > +formats when enabled. Parallel decompression is somewhat faster,
> > but the true
> > +speedup comes during compression.")
> > + (license license:expat))))
> > +
> > (define-public blasr-libcpp
> > (package
> > (name "blasr-libcpp")
> > --
> > 2.31.1
> >
>
> Looks good to me!
>
Thank you Efraim, and thank you Xinglu Chen.
I pushed this patch.
Kind regards,
Roel Janssen
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