diff options
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 12 | ||||
| -rw-r--r-- | gnu/packages/patches/khmer-use-libraries.patch | 16 |
3 files changed, 9 insertions, 20 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 4c54f024e0..a467501f50 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -951,7 +951,6 @@ dist_patch_DATA = \ %D%/packages/patches/java-xerces-xjavac_taskdef.patch \ %D%/packages/patches/jbig2dec-ignore-testtest.patch \ %D%/packages/patches/kdbusaddons-kinit-file-name.patch \ - %D%/packages/patches/khmer-use-libraries.patch \ %D%/packages/patches/libziparchive-add-includes.patch \ %D%/packages/patches/localed-xorg-keyboard.patch \ %D%/packages/patches/kiki-level-selection-crash.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f1a73bca7e..4f4d3d9839 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4168,7 +4168,7 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (define-public khmer (package (name "khmer") - (version "2.1.2") + (version "3.0.0a3") (source (origin (method git-fetch) @@ -4178,8 +4178,7 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (file-name (git-file-name name version)) (sha256 (base32 - "02x38d9jw2r58y8dmnj4hffy9wxv1yc1jwbvdbhby9dxndv94r9m")) - (patches (search-patches "khmer-use-libraries.patch")) + "01l4jczglkl7yfhgvzx8j0df7k54bk1r8sli9ll16i1mis0d8f37")) (modules '((guix build utils))) (snippet '(begin @@ -4192,6 +4191,12 @@ command, or queried for specific k-mers with @code{jellyfish query}.") ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html (delete-file-recursively "third-party/zlib") (delete-file-recursively "third-party/bzip2") + (delete-file-recursively "third-party/seqan") + (substitute* "setup.cfg" + (("# libraries = z,bz2") + "libraries = z,bz2") + (("include:third-party/zlib:third-party/bzip2") + "include:")) #t)))) (build-system python-build-system) (arguments @@ -4208,6 +4213,7 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (inputs `(("zlib" ,zlib) ("bzip2" ,bzip2) + ("seqan" ,seqan-1) ("python-screed" ,python-screed) ("python-bz2file" ,python-bz2file))) (home-page "https://khmer.readthedocs.org/") diff --git a/gnu/packages/patches/khmer-use-libraries.patch b/gnu/packages/patches/khmer-use-libraries.patch deleted file mode 100644 index 47d163a99a..0000000000 --- a/gnu/packages/patches/khmer-use-libraries.patch +++ /dev/null @@ -1,16 +0,0 @@ -Change setup.cfg so that the bundled zlib and bzip2 are not used. This cannot -currently be achieved using "--library z,bz2" as instructed in the setup.py. - -diff --git a/setup.cfg b/setup.cfg -index c054092..080992e 100644 ---- a/setup.cfg -+++ b/setup.cfg -@@ -1,7 +1,7 @@ - [build_ext] - define = SEQAN_HAS_BZIP2,SEQAN_HAS_ZLIB - undef = NO_UNIQUE_RC --# libraries = z,bz2 -+libraries = z,bz2 - ## if using system libraries - include-dirs = lib:third-party/zlib:third-party/bzip2:third-party/seqan/core/include:third-party/smhasher - # include-dirs = lib |