* [bug#61148] [PATCH 1/5] gnu: intervaltree: Update to 0.1-1.aa59377.
2023-01-29 13:09 [bug#61148] [PATCH 0/5] Update vcflib Efraim Flashner
@ 2023-01-29 13:12 ` Efraim Flashner
2023-01-29 13:12 ` [bug#61148] [PATCH 2/5] gnu: tabixpp: Update to 1.1.2 Efraim Flashner
` (4 subsequent siblings)
5 siblings, 0 replies; 7+ messages in thread
From: Efraim Flashner @ 2023-01-29 13:12 UTC (permalink / raw)
To: 61148; +Cc: Efraim Flashner
* gnu/packages/bioinformatics.scm (intervaltree): Update to
0.1-1.aa59377.
[arguments]: Fix cross-compiling.
---
gnu/packages/bioinformatics.scm | 17 ++++++++++-------
1 file changed, 10 insertions(+), 7 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8c75607a65..5cea726f8e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13632,10 +13632,10 @@ (define-public gffcompare
license:artistic2.0))))) ;license for gclib
(define-public intervaltree
- (let ((commit "b90527f9e6d51cd36ecbb50429e4524d3a418ea5"))
+ (let ((commit "aa5937755000f1cd007402d03b6f7ce4427c5d21"))
(package
(name "intervaltree")
- (version (git-version "0.0.0" "1" commit))
+ (version (git-version "0.1" "1" commit))
(source
(origin
(method git-fetch)
@@ -13644,15 +13644,18 @@ (define-public intervaltree
(commit commit)))
(file-name (git-file-name name version))
(sha256
- (base32 "0rgv6q5fl4x5d74n6p5wvdna6zmbdbqpb4jqqh6vq3670gn08xad"))))
+ (base32 "0p9aphy6sc01dg67xzqpnhvjmk21xa380bpfbkz24a23s6krhjwl"))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f ; No tests.
+ (list
+ #:tests? #f ; No tests.
#:make-flags
- ,#~(list (string-append "PREFIX=" #$output) "DESTDIR=\"\"")
+ #~(list (string-append "PREFIX=" #$output)
+ (string-append "CXX=" #$(cxx-for-target))
+ "DESTDIR=")
#:phases
- (modify-phases %standard-phases
- (delete 'configure)))) ; There is no configure phase.
+ #~(modify-phases %standard-phases
+ (delete 'configure)))) ; There is no configure phase.
(home-page "https://github.com/ekg/intervaltree")
(synopsis "Minimal C++ interval tree implementation")
(description "An interval tree can be used to efficiently find a set of
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
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^ permalink raw reply related [flat|nested] 7+ messages in thread* [bug#61148] [PATCH 2/5] gnu: tabixpp: Update to 1.1.2.
2023-01-29 13:09 [bug#61148] [PATCH 0/5] Update vcflib Efraim Flashner
2023-01-29 13:12 ` [bug#61148] [PATCH 1/5] gnu: intervaltree: Update to 0.1-1.aa59377 Efraim Flashner
@ 2023-01-29 13:12 ` Efraim Flashner
2023-01-29 13:12 ` [bug#61148] [PATCH 3/5] gnu: Add wfa2-lib Efraim Flashner
` (3 subsequent siblings)
5 siblings, 0 replies; 7+ messages in thread
From: Efraim Flashner @ 2023-01-29 13:12 UTC (permalink / raw)
To: 61148; +Cc: Efraim Flashner
* gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.2.
[source]: Add snippet to keep library name the same.
[arguments]: Adjust the make-flags to find htslib. Enable the tests.
Remove custom 'build-libraries phase, it is built by default now. Add a
phase to symlink the shared library to a generic .so name. Don't
override the 'install phase. Add a phase after 'install to create a
pkg-config file.
---
gnu/packages/bioinformatics.scm | 60 ++++++++++++++++++---------------
1 file changed, 33 insertions(+), 27 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5cea726f8e..fa0a6c0dd6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4,7 +4,7 @@
;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016, 2020, 2021 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016-2023 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -15640,7 +15640,7 @@ (define-public tbsp
(define-public tabixpp
(package
(name "tabixpp")
- (version "1.1.0")
+ (version "1.1.2")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -15648,43 +15648,47 @@ (define-public tabixpp
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1k2a3vbq96ic4lw72iwp5s3mwwc4xhdffjj584yn6l9637q9j1yd"))
+ (base32 "00aqs147yn8zcvxims5njwxqsbnlbjv7lnmiwqy80bfdcbhljkqf"))
(modules '((guix build utils)))
(snippet
#~(begin
- (delete-file-recursively "htslib")))))
+ (delete-file-recursively "htslib")
+ ;; Keep it named tabixpp.
+ (substitute* "Makefile"
+ (("libtabix") "libtabixpp"))))))
(build-system gnu-build-system)
- (inputs
- (list bzip2 htslib xz zlib))
(arguments
(list #:make-flags #~(list (string-append "CC=" #$(cc-for-target))
(string-append "CXX=" #$(cxx-for-target))
+ (string-append "AR=" #$(ar-for-target))
"HTS_HEADERS="
- (string-append "HTS_LIB="
- (search-input-file %build-inputs
- "/lib/libhts.a"))
- "INCLUDES=")
- #:tests? #f ; There are no tests to run.
+ "HTS_LIB="
+ (string-append
+ "INCLUDES= -I"
+ (search-input-directory %build-inputs
+ "include/htslib"))
+ (string-append
+ "LIBPATH= -L. -L"
+ (dirname
+ (search-input-file %build-inputs
+ "/lib/libhts.a")))
+ (string-append "PREFIX=" #$output)
+ "DESTDIR=")
+ #:test-target "test"
#:phases
#~(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase.
- ;; Build shared and static libraries.
- (add-after 'build 'build-libraries
- (lambda* (#:key inputs #:allow-other-keys)
- (invoke #$(cxx-for-target)
- "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts")
- (invoke #$(ar-for-target) "rcs" "libtabixpp.a" "tabix.o")))
- (replace 'install
+ (add-after 'install 'symlink-shared-library
+ (lambda* (#:key outputs #:allow-other-keys)
+ (with-directory-excursion
+ (string-append (assoc-ref outputs "out") "/lib")
+ (symlink "libtabixpp.so.1" "libtabixpp.so"))))
+ (add-after 'install 'make-pkg-config-file
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
- (lib (string-append out "/lib"))
- (bin (string-append out "/bin")))
- (install-file "tabix++" bin)
- (install-file "libtabixpp.so" lib)
- (install-file "libtabixpp.a" lib)
- (install-file "tabix.hpp" (string-append out "/include"))
- (mkdir-p (string-append lib "/pkgconfig"))
- (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc")
+ (pkgconfig (string-append out "/lib/pkgconfig")))
+ (mkdir-p pkgconfig)
+ (with-output-to-file (string-append pkgconfig "/tabixpp.pc")
(lambda _
(format #t "prefix=~a~@
exec_prefix=${prefix}~@
@@ -15692,12 +15696,14 @@ (define-public tabixpp
includedir=${prefix}/include~@
~@
~@
- Name: libtabixpp~@
+ Name: tabixpp~@
Version: ~a~@
Description: C++ wrapper around tabix project~@
Libs: -L${libdir} -ltabixpp~@
Cflags: -I${includedir}~%"
out #$version)))))))))
+ (inputs
+ (list bzip2 curl htslib xz zlib))
(home-page "https://github.com/ekg/tabixpp")
(synopsis "C++ wrapper around tabix project")
(description "This is a C++ wrapper around the Tabix project which abstracts
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351
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^ permalink raw reply related [flat|nested] 7+ messages in thread* [bug#61148] [PATCH 3/5] gnu: Add wfa2-lib.
2023-01-29 13:09 [bug#61148] [PATCH 0/5] Update vcflib Efraim Flashner
2023-01-29 13:12 ` [bug#61148] [PATCH 1/5] gnu: intervaltree: Update to 0.1-1.aa59377 Efraim Flashner
2023-01-29 13:12 ` [bug#61148] [PATCH 2/5] gnu: tabixpp: Update to 1.1.2 Efraim Flashner
@ 2023-01-29 13:12 ` Efraim Flashner
2023-01-29 13:12 ` [bug#61148] [PATCH 4/5] gnu: Add libvcfh Efraim Flashner
` (2 subsequent siblings)
5 siblings, 0 replies; 7+ messages in thread
From: Efraim Flashner @ 2023-01-29 13:12 UTC (permalink / raw)
To: 61148; +Cc: Efraim Flashner
* gnu/packages/bioinformatics.scm (wfa2-lib): New variable.
---
gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fa0a6c0dd6..7b5d5c5e8c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15710,6 +15710,40 @@ (define-public tabixpp
some of the details of opening and jumping in tabix-indexed files.")
(license license:expat)))
+(define-public wfa2-lib
+ (let ((commit "188b522ae634add3c692ca7547595b7266f1fa19")
+ (revision "1"))
+ (package
+ (name "wfa2-lib")
+ (version (git-version "2.3.1" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/smarco/WFA2-lib")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1pq844zsl7v5zk6pzkbh5j2k2g1ac54nlvgyihla2wlwi0ibndax"))))
+ (build-system cmake-build-system)
+ (arguments
+ (list
+ #:configure-flags
+ #~(list "-DOPENMP=ON")))
+ (native-inputs
+ (list pkg-config))
+ (home-page "https://github.com/ekg/tabixpp")
+ (synopsis "Wavefront alignment algorithm library")
+ (description "The @acronym{wavefront alignment, WFA} algorithm is an exact
+gap-affine algorithm that takes advantage of homologous regions between the
+sequences to accelerate the alignment process. Unlike to traditional dynamic
+programming algorithms that run in quadratic time, the WFA runs in time
+@code{O(ns+s^2)}, proportional to the sequence length @code{n} and the alignment
+score @code{s}, using @code{O(s^2)} memory (or @code{O(s)} using the
+ultralow/BiWFA mode). Moreover, the WFA algorithm exhibits simple computational
+patterns that the modern compilers can automatically vectorize for different
+architectures without adapting the code.")
+ (license license:expat))))
+
(define-public smithwaterman
(let ((commit "2610e259611ae4cde8f03c72499d28f03f6d38a7"))
(package
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
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^ permalink raw reply related [flat|nested] 7+ messages in thread* [bug#61148] [PATCH 4/5] gnu: Add libvcfh.
2023-01-29 13:09 [bug#61148] [PATCH 0/5] Update vcflib Efraim Flashner
` (2 preceding siblings ...)
2023-01-29 13:12 ` [bug#61148] [PATCH 3/5] gnu: Add wfa2-lib Efraim Flashner
@ 2023-01-29 13:12 ` Efraim Flashner
2023-01-29 13:12 ` [bug#61148] [PATCH 5/5] gnu: vcflib: Update to 1.0.6 Efraim Flashner
2023-10-27 12:38 ` [bug#61148] [PATCH 0/5] Update vcflib Ricardo Wurmus
5 siblings, 0 replies; 7+ messages in thread
From: Efraim Flashner @ 2023-01-29 13:12 UTC (permalink / raw)
To: 61148; +Cc: Efraim Flashner
* gnu/packages/bioinformatics.scm (libvcfh): New variable.
---
gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++
1 file changed, 37 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7b5d5c5e8c..05a07af7f3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15744,6 +15744,43 @@ (define-public wfa2-lib
architectures without adapting the code.")
(license license:expat))))
+(define-public libvcfh
+ (let ((commit "44b6580639a216a484fd96de75a839091f25768a")
+ (revision "1"))
+ (package
+ (name "libvcfh")
+ (version (git-version "0.0.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/edawson/libVCFH.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0jjqnzvai0849czh1hi5inm6y0228cw2s97i76f3vhyxj21mzvwm"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (delete 'configure) ; No configure script
+ (replace 'check
+ (lambda* (#:key tests? make-flags #:allow-other-keys)
+ (when tests?
+ (apply invoke "make" "test" make-flags)
+ (invoke "./test"))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (install-file "libvcfh.a" (string-append out "/lib"))
+ (install-file "vcfheader.hpp"
+ (string-append out "/include/libvcfh"))))))))
+ (home-page "https://github.com/edawson/libVCFH")
+ (synopsis "Library for generating VCF headers")
+ (description "@code{libVCFH} is a set of data structures you can populate
+to print a VCf header. It should be in spec with VCF4.1/4.2.")
+ (license license:expat))))
+
(define-public smithwaterman
(let ((commit "2610e259611ae4cde8f03c72499d28f03f6d38a7"))
(package
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
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^ permalink raw reply related [flat|nested] 7+ messages in thread* [bug#61148] [PATCH 5/5] gnu: vcflib: Update to 1.0.6.
2023-01-29 13:09 [bug#61148] [PATCH 0/5] Update vcflib Efraim Flashner
` (3 preceding siblings ...)
2023-01-29 13:12 ` [bug#61148] [PATCH 4/5] gnu: Add libvcfh Efraim Flashner
@ 2023-01-29 13:12 ` Efraim Flashner
2023-10-27 12:38 ` [bug#61148] [PATCH 0/5] Update vcflib Ricardo Wurmus
5 siblings, 0 replies; 7+ messages in thread
From: Efraim Flashner @ 2023-01-29 13:12 UTC (permalink / raw)
To: 61148; +Cc: Efraim Flashner
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.6.
[source]: Adjust snippet to use unbundled wfa2-lib include directory.
Also unbundle simde, wfa2-lib. Remove googletest from unbundle list, it
is no longer in use.
[inputs]: Add curl, simde, wfa2-lib.
[native-inputs]: Add pybind11, pandoc when available. Add the sources
for libvcfh.
[arguments]: Adjust configure-flags to build without zig and to use the
unbundled wfa2-lib. Adjust custom 'build-shared-library phase for
changes in the source. Adjust custom 'unpack-submodule-sources for
changes in the source.
---
gnu/packages/bioinformatics.scm | 69 +++++++++++++++++++++++++--------
1 file changed, 52 insertions(+), 17 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 05a07af7f3..c4eeb6d68f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -16033,74 +16033,108 @@ (define-public fastahack
(define-public vcflib
(package
(name "vcflib")
- (version "1.0.3")
+ (version "1.0.6")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/vcflib/vcflib")
- (commit (string-append "v" version))))
+ (commit (string-append "v" version))
+ (recursive? #t)))
(file-name (git-file-name name version))
(sha256
- (base32 "1r7pnajg997zdjkf1b38m14v0zqnfx52w7nbldwh1xpbpahb1hjh"))
+ (base32 "0zcs8j3vdajram53srvjmq353f3prqdbn8fvzja4412w4zay79fz"))
(modules '((guix build utils)))
(snippet
#~(begin
(substitute* "CMakeLists.txt"
((".*fastahack.*") "")
((".*smithwaterman.*") "")
+ ;; Also look for fastahack and smithwaterman since
+ ;; we've just unbundled them.
(("(pkg_check_modules\\(TABIXPP)" text)
(string-append
"pkg_check_modules(FASTAHACK REQUIRED fastahack)\n"
"pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n"
text))
+ ;; Also link vcflib to fastahack and smithwaterman.
(("\\$\\{TABIXPP_LIBRARIES\\}" text)
(string-append "${FASTAHACK_LIBRARIES} "
"${SMITHWATERMAN_LIBRARIES} "
- text)))
+ text))
+ ;; Honor setting WFA_INCLUDE_DIRS and not look at
+ ;; PREFIX/include/wfa2lib.
+ (((string-append "\\$\\{CMAKE_INSTALL_PREFIX\\}/"
+ "\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}/wfa2lib"))
+ "${WFA_INCLUDE_DIRS}"))
(substitute* (find-files "." "\\.(h|c)(pp)?$")
(("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>")
(("\"convert.h\"") "<smithwaterman/convert.h>")
(("\"disorder.h\"") "<smithwaterman/disorder.h>")
(("Fasta.h") "fastahack/Fasta.h"))
- (for-each delete-file-recursively
- '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree"
- "libVCFH" "multichoose" "smithwaterman"))))))
+ (substitute* "src/Variant.h"
+ (("wavefront/wfa.hpp") "wfa2lib/wavefront/wfa.hpp"))
+ (delete-file-recursively "src/simde")
+ (with-directory-excursion "contrib"
+ (for-each delete-file-recursively
+ '(;"c-progress-bar"
+ "fastahack"
+ "filevercmp"
+ "fsom"
+ "intervaltree"
+ "libVCFH"
+ "multichoose"
+ "smithwaterman"
+ "tabixpp"
+ "WFA2-lib")))))))
(build-system cmake-build-system)
(inputs
(list bzip2
+ curl
htslib
fastahack
perl
python
+ simde
smithwaterman
tabixpp
+ wfa2-lib
xz
zlib))
(native-inputs
`(("pkg-config" ,pkg-config)
+ ("pybind11" ,pybind11)
+ ,@(if (member (%current-system)
+ (package-transitive-supported-systems pandoc))
+ `(("pandoc" ,pandoc))
+ '())
;; Submodules.
- ;; This package builds against the .o files so we need to extract the source.
+ ;; Not all of these packages provide libraries to link against.
("filevercmp-src" ,(package-source filevercmp))
("fsom-src" ,(package-source fsom))
("intervaltree-src" ,(package-source intervaltree))
+ ("libvcfh-src" ,(package-source libvcfh))
("multichoose-src" ,(package-source multichoose))))
(arguments
(list #:configure-flags
- #~(list (string-append
+ #~(list "-DZIG=NO"
+ "-DWFA_GITMODULE=OFF"
+ (string-append "-DWFA_INCLUDE_DIRS="
+ (search-input-directory %build-inputs
+ "include/wfa2lib"))
+ "-DTABIX_FOUND=ON" ; Default to found
+ (string-append
"-DPKG_CONFIG_EXECUTABLE="
(search-input-file
%build-inputs (string-append
"/bin/" #$(pkg-config-for-target)))))
- #:tests? #f ; no tests
+ #:tests? #f ; Tests need more configuring.
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'build-shared-library
(lambda _
(substitute* "CMakeLists.txt"
- (("vcflib STATIC") "vcflib SHARED"))
- (substitute* "test/Makefile"
- (("libvcflib.a") "libvcflib.so"))))
+ (("vcflib STATIC") "vcflib SHARED"))))
(add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs native-inputs #:allow-other-keys)
(let ((unpack (lambda (source target)
@@ -16114,10 +16148,11 @@ (define-public vcflib
source
"--strip-components=1")))))))
(and
- (unpack "filevercmp-src" "filevercmp")
- (unpack "fsom-src" "fsom")
- (unpack "intervaltree-src" "intervaltree")
- (unpack "multichoose-src" "multichoose")))))
+ (unpack "filevercmp-src" "contrib/filevercmp")
+ (unpack "fsom-src" "contrib/fsom")
+ (unpack "intervaltree-src" "contrib/intervaltree")
+ (unpack "libvcfh-src" "contrib/libvcfh")
+ (unpack "multichoose-src" "contrib/multichoose")))))
;; This pkg-config file is provided by other distributions.
(add-after 'install 'install-pkg-config-file
(lambda* (#:key outputs #:allow-other-keys)
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351
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^ permalink raw reply related [flat|nested] 7+ messages in thread* [bug#61148] [PATCH 0/5] Update vcflib
2023-01-29 13:09 [bug#61148] [PATCH 0/5] Update vcflib Efraim Flashner
` (4 preceding siblings ...)
2023-01-29 13:12 ` [bug#61148] [PATCH 5/5] gnu: vcflib: Update to 1.0.6 Efraim Flashner
@ 2023-10-27 12:38 ` Ricardo Wurmus
5 siblings, 0 replies; 7+ messages in thread
From: Ricardo Wurmus @ 2023-10-27 12:38 UTC (permalink / raw)
To: 61148
These patches look good to me.
One note: you can use #$output directly instead of (assoc-ref outputs "out").
--
Ricardo
^ permalink raw reply [flat|nested] 7+ messages in thread