diff options
author | Ben Woodcroft <donttrustben@gmail.com> | 2018-09-22 08:19:09 +1000 |
---|---|---|
committer | Ben Woodcroft <donttrustben@gmail.com> | 2018-09-22 09:16:47 +1000 |
commit | 05fb1e0017030f1c0cbc7e9a1adeccca57ef1d9d (patch) | |
tree | 8d6f02eee6074d0243589ea5a6939a0bfcac06f4 /gnu | |
parent | 78b7b9dbe9098c9c47c7acba363223bb6c5bb1c8 (diff) | |
download | guix-05fb1e0017030f1c0cbc7e9a1adeccca57ef1d9d.tar.gz |
gnu: hmmer: Update to 3.2.1.
* gnu/packages/bioinformatics.scm (hmmer): Update to 3.2.1. [origin]: Remove patch. [license]: Change to BSD-3. [supported-systems]: New field. * gnu/packages/patches/hmmer-remove-cpu-specificity.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
Diffstat (limited to 'gnu')
-rw-r--r-- | gnu/local.mk | 1 | ||||
-rw-r--r-- | gnu/packages/bioinformatics.scm | 19 | ||||
-rw-r--r-- | gnu/packages/patches/hmmer-remove-cpu-specificity.patch | 22 |
3 files changed, 7 insertions, 35 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 4097ad5fcd..daf96ea4b6 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -805,7 +805,6 @@ dist_patch_DATA = \ %D%/packages/patches/hdf-eos5-remove-gctp.patch \ %D%/packages/patches/hdf-eos5-fix-szip.patch \ %D%/packages/patches/hdf-eos5-fortrantests.patch \ - %D%/packages/patches/hmmer-remove-cpu-specificity.patch \ %D%/packages/patches/higan-remove-march-native-flag.patch \ %D%/packages/patches/hubbub-sort-entities.patch \ %D%/packages/patches/hurd-fix-eth-multiplexer-dependency.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9599e3096f..b619866ba3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2936,18 +2936,15 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") (define-public hmmer (package (name "hmmer") - (version "3.1b2") + (version "3.2.1") (source (origin (method url-fetch) (uri (string-append - "http://eddylab.org/software/hmmer" - (version-major version) "/" - version "/hmmer-" version ".tar.gz")) + "http://eddylab.org/software/hmmer/hmmer-" version ".tar.gz")) (sha256 (base32 - "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx")) - (patches (search-patches "hmmer-remove-cpu-specificity.patch")))) + "171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl))) (home-page "http://hmmer.org/") @@ -2957,12 +2954,10 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).") - (license (list license:gpl3+ - ;; The bundled library 'easel' is distributed - ;; under The Janelia Farm Software License. - (license:non-copyleft - "file://easel/LICENSE" - "See easel/LICENSE in the distribution."))))) + ;; hmmer uses non-portable SSE intrinsics so building fails on other + ;; platforms. + (supported-systems '("x86_64-linux" "i686-linux")) + (license license:bsd-3))) (define-public htseq (package diff --git a/gnu/packages/patches/hmmer-remove-cpu-specificity.patch b/gnu/packages/patches/hmmer-remove-cpu-specificity.patch deleted file mode 100644 index ba98db4d0e..0000000000 --- a/gnu/packages/patches/hmmer-remove-cpu-specificity.patch +++ /dev/null @@ -1,22 +0,0 @@ -This patch removes compilation flags which make the build for the machine -where compilation takes place, rendering the build not reproducible. - -diff --git a/configure b/configure -index 8b6aaef..49a6afc 100755 ---- a/configure -+++ b/configure -@@ -6125,14 +6125,6 @@ fi # guess arch - - if test "x$ax_gcc_arch" != x -a "x$ax_gcc_arch" != xno; then - for arch in $ax_gcc_arch; do -- if test "x$acx_maxopt_portable" = xyes; then # if we require portable code -- flags="-mtune=$arch" -- # -mcpu=$arch and m$arch generate nonportable code on every arch except -- # x86. And some other arches (e.g. Alpha) don't accept -mtune. Grrr. -- case $host_cpu in i*86|x86_64*) flags="$flags -mcpu=$arch -m$arch";; esac -- else -- flags="-march=$arch -mcpu=$arch -m$arch" -- fi - for flag in $flags; do - as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$flag" | $as_tr_sh` - { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts $flag" >&5 |