[-- Attachment #1: Type: text/plain, Size: 172 bytes --] 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 [-- Attachment #2: 0001-gnu-Add-pbgzip.patch --] [-- Type: text/x-patch, Size: 3186 bytes --] From 3d34e82ee67f5ee0b226de350f40d7f881169a56 Mon Sep 17 00:00:00 2001 From: Roel Janssen <roel@gnu.org> Date: Wed, 21 Apr 2021 14:24:07 +0200 Subject: [PATCH] gnu: Add pbgzip. * gnu/packages/bioinformatics.scm (pbgzip): New variable. --- gnu/packages/bioinformatics.scm | 42 ++++++++++++++++++++++++++++++++- 1 file changed, 41 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 31205c473a..35601378c2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> -;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org> +;;; Copyright © 2016, 2020, 2021 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com> @@ -569,6 +569,46 @@ 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 (string-take commit 7)) + (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) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'autogen + (lambda _ + (zero? (system* "sh" "autogen.sh"))))))) + (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.") + (license license:expat)))) + (define-public blasr-libcpp (package (name "blasr-libcpp") -- 2.31.1
[-- Attachment #1: Type: text/plain, Size: 1257 bytes --] 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. [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 861 bytes --]
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.
[-- Attachment #1: Type: text/plain, Size: 723 bytes --] 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. [-- Attachment #2: This is a digitally signed message part --] [-- Type: application/pgp-signature, Size: 260 bytes --]
[-- Attachment #1: Type: text/plain, Size: 1116 bytes --] 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. -- Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 833 bytes --]
[-- Attachment #1: Type: text/plain, Size: 1214 bytes --] 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 [-- Attachment #2: 0001-gnu-Add-pbgzip.patch --] [-- Type: text/x-patch, Size: 2986 bytes --] From b03f8d8926cdd6a28502f2bdc6db74854144f050 Mon Sep 17 00:00:00 2001 From: Roel Janssen <roel@gnu.org> Date: Thu, 29 Apr 2021 14:18:30 +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..8c4d0fc649 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> -;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org> +;;; Copyright © 2016, 2020, 2021 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@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 (string-take commit 7)) + (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.") + (license license:expat)))) + (define-public blasr-libcpp (package (name "blasr-libcpp") -- 2.31.1
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?
[-- Attachment #1: Type: text/plain, Size: 2632 bytes --] 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 [-- Attachment #2: 0001-gnu-Add-pbgzip.patch --] [-- Type: text/x-patch, Size: 2991 bytes --] From 1af29f66980ba19740e05a27135f141e23b7fd3f Mon Sep 17 00:00:00 2001 From: Roel Janssen <roel@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@gmail.com> ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> -;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org> +;;; Copyright © 2016, 2020, 2021 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@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 +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
[-- Attachment #1: Type: text/plain, Size: 6447 bytes --] 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@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@gmail.com> > ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl> > ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> > -;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org> > +;;; Copyright © 2016, 2020, 2021 Roel Janssen <roel@gnu.org> > ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il> > ;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com> > ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@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! -- Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 833 bytes --]
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@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