guix/gnu/packages
Ricardo Wurmus 94ce537eac gnu: Add TopHat.
* gnu/packages/bioinformatics.scm (tophat): New variable.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
2016-01-23 08:53:10 +01:00
..
bootstrap
patches gnu: Add TopHat. 2016-01-23 08:53:10 +01:00
abduco.scm
abiword.scm
acct.scm
acl.scm
admin.scm gnu: Add iftop. 2016-01-21 20:21:19 -05:00
adns.scm
aidc.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
algebra.scm gnu: arb: Update to 2.8.1. 2016-01-20 16:33:34 +01:00
animation.scm gnu: Add Synfig Studio. 2015-11-20 20:23:03 +01:00
apl.scm
apr.scm
aria2.scm gnu: Add c-ares. 2015-11-12 16:21:00 +02:00
asciidoc.scm
aspell.scm
attr.scm
audacity.scm
audio.scm gnu: libxmp: Update to 4.3.10. 2016-01-21 00:44:46 -05:00
autogen.scm gnu: autogen: Update to 5.18.7. 2015-12-08 14:30:29 +02:00
autotools.scm
avahi.scm
avr.scm gnu: Add microscheme. 2015-11-11 22:40:50 +01:00
backup.scm
base.scm
bash.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
bdw-gc.scm gnu: Add Asymptote. 2016-01-02 16:04:55 -06:00
bioinformatics.scm gnu: Add TopHat. 2016-01-23 08:53:10 +01:00
bison.scm
bittorrent.scm gnu: Add transmission-remote-cli. 2016-01-20 20:19:46 -05:00
boost.scm gnu: boost: Update to 1.60.0. 2016-01-12 21:07:53 +01:00
bootstrap.scm
busybox.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
calcurse.scm
calendar.scm gnu: Add khal. 2016-01-15 16:45:24 -05:00
ccache.scm
cdrom.scm gnu: libcue: Update source URL. 2015-12-30 19:59:58 -05:00
certs.scm
check.scm
ci.scm
cmake.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
code.scm gnu: global: Use modify-phases syntax. 2016-01-12 14:47:10 +02:00
commencement.scm build-system/gnu: Make 'package-with-explicit-inputs' idempotent. 2016-01-06 23:08:22 +01:00
compression.scm
conkeror.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
conky.scm
cook.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
cpio.scm
cppi.scm
cross-base.scm
crypto.scm gnu: libsodium: Add alternate URL. 2015-12-25 23:56:15 -05:00
cryptsetup.scm
cups.scm gnu: cups-filters: Update to 1.4.0. (fixes CVE-2015-8560) 2015-12-26 11:01:01 -05:00
curl.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
cyrus-sasl.scm
databases.scm gnu: mariadb: Update to 10.0.23. 2016-01-18 01:43:07 -05:00
datamash.scm gnu: datamash: Update to 1.1.0. 2016-01-18 12:14:20 +02:00
datastructures.scm gnu: Move sparsehash to datastructures module. 2015-12-11 15:59:20 +01:00
dav.scm gnu: Add vdirsyncer. 2016-01-15 16:45:24 -05:00
dc.scm
debug.scm gnu: american-fuzzy-lop: Update to 1.96b. 2016-01-21 23:54:48 -06:00
dejagnu.scm
dico.scm gnu: dico: Sort entries in .a files deterministically. 2015-11-25 11:59:54 +01:00
dictionaries.scm gnu: Do not #:select from (gnu packages …) modules. 2015-12-19 00:22:42 +01:00
disk.scm gnu: Do not #:select from (gnu packages …) modules. 2015-12-19 00:22:42 +01:00
djvu.scm
dns.scm gnu: bind-utils: Build and install "nsupdate". 2016-01-21 15:53:35 +01:00
docbook.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
docker.scm gnu: Add docker-compose. 2016-01-14 09:17:12 -05:00
doxygen.scm
dunst.scm
dvtm.scm
ebook.scm gnu: calibre: Update to 2.48.0. 2016-01-05 22:46:54 +01:00
ed.scm
elf.scm
emacs.scm gnu: magit: Update to 2.4.0. 2016-01-18 22:40:33 +03:00
enchant.scm
engineering.scm gnu: Add Fritzing. 2015-12-30 20:41:33 +01:00
enlightenment.scm gnu: enlightenment: Update to 0.20.3. 2016-01-20 12:37:21 +02:00
fcitx.scm
feh.scm
figlet.scm
file.scm
finance.scm
firmware.scm gnu: Fix a few 'source-file-name' lint warnings. 2015-11-23 10:52:32 +01:00
fish.scm
flashing-tools.scm
flex.scm
fltk.scm
fonts.scm gnu: font-adobe-source-han-sans: Update to 1.004. 2015-11-04 16:02:14 +08:00
fontutils.scm
freedesktop.scm gnu: Add colord-gtk. 2015-12-20 18:59:21 +08:00
freeipmi.scm gnu: freeipmpi: Update to 1.5.1. 2015-12-02 20:32:30 +02:00
fribidi.scm
ftp.scm
fvwm.scm
game-development.scm gnu: love: Update to 0.10.0. 2016-01-02 10:31:53 +08:00
games.scm gnu: manaplus: Update to 1.6.1.16. 2016-01-18 22:40:33 +03:00
gawk.scm
gcal.scm
gcc.scm gnu: gcc-5: Update to 5.3.0. 2015-12-14 07:32:01 +02:00
gd.scm
gdb.scm gnu: gdb: Update to 7.10.1. 2015-12-06 15:57:33 +02:00
geeqie.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
gettext.scm
ghostscript.scm
gimp.scm gnu: Do not #:select from (gnu packages …) modules. 2015-12-19 00:22:42 +01:00
gkrellm.scm
gl.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
glib.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
gnome.scm gnu: glade: Update to 3.18.5. 2016-01-15 22:29:37 +01:00
gnu-pw-mgr.scm
gnucash.scm gnu: gnucash: Update to 2.6.9. 2015-11-16 04:15:02 +01:00
gnunet.scm gnu: libmicrohttpd: Update to 0.9.48. 2015-12-22 22:50:58 +02:00
gnupg.scm gnu: gnupg: Add TOFU support. 2016-01-14 15:05:36 +02:00
gnustep.scm
gnuzilla.scm gnu: icecat: Update to 38.5.2-gnu1. 2016-01-09 22:51:28 +01:00
gperf.scm
gprolog.scm
gps.scm
graphics.scm gnu: boost: Update to 1.60.0. 2016-01-12 21:07:53 +01:00
graphviz.scm
groff.scm
grub.scm gnu: grub: Add fix for CVE-2015-8730. 2015-12-21 12:33:55 -05:00
grue-hunter.scm
gsasl.scm
gstreamer.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
gtk.scm gnu: gtk+: Add patch to support GUIX_GTK3_PATH. 2016-01-04 16:11:10 -05:00
guile-wm.scm
guile.scm gnu: Add g-wrap. 2015-12-13 15:20:44 +01:00
gv.scm
gxmessage.scm
haskell.scm gnu: Use #:prefix when importing (guix licenses). 2015-12-19 00:34:00 +01:00
hugs.scm
hurd.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
ibus.scm
icu4c.scm
idutils.scm
image.scm gnu: libpng: Update to 1.5.26 [fixes CVE-2015-8472 and CVE-2015-8540]. 2015-12-26 11:01:01 -05:00
imagemagick.scm gnu: Add GraphicsMagick. 2015-11-17 08:43:32 +01:00
indent.scm
inklingreader.scm gnu: Add inklingreader. 2015-11-12 15:57:02 +01:00
inkscape.scm
irssi.scm gnu: irssi: Update source URL. 2015-12-27 17:39:03 -05:00
iso-codes.scm
java.scm gnu: icedtea-6: Fix directory name in "unpack" phase. 2016-01-12 11:39:21 +01:00
jemalloc.scm
jrnl.scm
julia.scm gnu: julia: Update to 0.4.3. 2016-01-13 17:05:38 +01:00
kde-frameworks.scm
kde.scm
key-mon.scm gnu: key-mon: Remove unnecessary propagated inputs. 2015-12-18 11:04:22 +01:00
kodi.scm gnu: Add and use default IcedTea. 2016-01-06 11:38:50 +01:00
language.scm
ld-wrapper.in
ldc.scm gnu: ldc: Fix license. 2016-01-06 14:21:53 +01:00
lego.scm gnu: Add NQC. 2016-01-20 22:06:27 -06:00
less.scm
lesstif.scm
libcanberra.scm
libdaemon.scm
libedit.scm
libevent.scm gnu: libev: Update source URL. 2015-12-25 23:51:08 -05:00
libffcall.scm
libffi.scm
libftdi.scm
libidn.scm
libphidget.scm
libreoffice.scm gnu: boost: Update to 1.60.0. 2016-01-12 21:07:53 +01:00
libsigsegv.scm
libunistring.scm
libunwind.scm
libupnp.scm
libusb.scm
lightning.scm
links.scm
linux-libre-i686.conf gnu: linux-libre: Update to 4.4. 2016-01-11 19:13:37 -05:00
linux-libre-x86_64.conf gnu: linux-libre: Update to 4.4. 2016-01-11 19:13:37 -05:00
linux.scm gnu: fuse: Update to 2.9.5 [fixes CVE-2016-1233]. 2016-01-22 09:00:34 +02:00
lirc.scm
lisp.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
llvm.scm gnu: clang-runtime: Mark MIPS as unsupported. 2015-11-04 09:28:46 +01:00
lout.scm
lsh.scm
lsof.scm
lua.scm gnu: Build lua-5.2 with a dynamic library 2015-11-08 22:21:19 +01:00
lxde.scm
lxqt.scm
lynx.scm gnu: lynx: Update source URL. 2015-12-25 23:58:33 -05:00
m4.scm
machine-learning.scm gnu: Add AdaptiveSparsity. 2015-12-21 16:05:38 +01:00
mail.scm gnu: fdm: Adjust license link to point to web-accessible copy of command.c 2016-01-19 07:54:18 -08:00
make-bootstrap.scm
man.scm gnu: man-pages: Update to 4.04. 2016-01-11 09:37:50 +02:00
markdown.scm
maths.scm gnu: gmsh: Update to 2.11.0. 2016-01-06 10:49:23 -06:00
mc.scm
mcrypt.scm
messaging.scm gnu: gajim: Update to 0.16.5 [fixes CVE-2015-8688]. 2016-01-21 10:24:44 -05:00
mg.scm
miscfiles.scm
mit-krb5.scm gnu: mit-krb5: Add fixes for CVE-2015-{2695,2696,2697,2698}. 2015-11-13 12:42:47 -05:00
moe.scm
moreutils.scm gnu: moreutils: Update to 0.57. 2015-12-25 23:59:26 -05:00
mp3.scm gnu: mp3info: Update URL. 2015-12-06 23:12:12 +01:00
mpd.scm
mpi.scm gnu: openmpi: Update to 1.10.1. 2015-11-20 11:58:40 -06:00
mtools.scm
multiprecision.scm
music.scm gnu: lilypond: Double 'max-silent-time'. 2016-01-19 22:14:15 +01:00
nano.scm gnu: nano: Update to 2.5.0. 2015-12-06 16:49:41 +02:00
ncdu.scm
ncurses.scm gnu: Add dialog. 2015-12-05 09:44:37 -05:00
netpbm.scm
nettle.scm
networking.scm
ninja.scm
node.scm gnu: node: Do not use bundled dependencies. 2015-12-07 17:05:34 -05:00
noweb.scm
ntp.scm gnu: Add tlsdate. 2015-12-19 23:16:18 +01:00
nutrition.scm
nvi.scm
ocaml.scm gnu: hevea: Update to 2.28. 2016-01-17 01:04:43 -06:00
ocr.scm
onc-rpc.scm
openbox.scm
openldap.scm
openstack.scm python2-jsonschema: Add python2-functools32 to inputs. 2016-01-18 17:23:37 +02:00
orpheus.scm
ots.scm
owncloud.scm gnu: owncloud-client: Update to 2.1.0. 2015-12-12 22:52:48 +02:00
package-management.scm gnu: guix: Update development snapshot to f888c0b. 2016-01-06 23:08:22 +01:00
parallel.scm gnu: parallel: Update to 20151222. 2015-12-22 22:47:44 +02:00
password-utils.scm gnu: Add libpwquality. 2015-12-18 10:30:16 +08:00
patchutils.scm gnu: colordiff: Update to 1.0.16. 2015-12-26 00:10:32 -05:00
pciutils.scm
pcre.scm gnu: pcre: Update to 8.38. 2015-12-07 09:54:01 -05:00
pdf.scm
pem.scm
perl.scm gnu: Add File::Slurp::Tiny. 2015-12-24 10:10:40 +01:00
photo.scm
pkg-config.scm
plotutils.scm gnu: Add Asymptote. 2016-01-02 16:04:55 -06:00
polkit.scm
popt.scm
pretty-print.scm
protobuf.scm
pth.scm
pulseaudio.scm gnu: libsndfile: Add fixes for CVE-2014-9496 and CVE-2015-7805. 2015-11-18 17:47:40 -05:00
pumpio.scm
pv.scm
python.scm python2-jsonschema: Add python2-functools32 to inputs. 2016-01-18 17:23:37 +02:00
qemu.scm gnu: Add qemu-minimal. 2015-11-21 00:36:23 +01:00
qt.scm gnu: Add qtkeychain. 2015-11-12 16:14:42 +02:00
ragel.scm gnu: Add Ragel. 2015-11-25 15:21:47 +01:00
ratpoison.scm
rc.scm
rdesktop.scm
rdf.scm
readline.scm
rrdtool.scm
rsync.scm gnu: rsync: Update to 3.1.2. 2016-01-17 21:44:31 -05:00
ruby.scm gnu: Add ruby-bio-commandeer. 2016-01-14 08:00:02 +10:00
rush.scm
samba.scm gnu: samba: Update to 4.3.3. 2016-01-03 14:59:49 -05:00
sawfish.scm
scanner.scm
scheme.scm
screen.scm gnu: Add byobu. 2015-11-03 17:08:41 -06:00
scribus.scm gnu: Add Scribus. 2015-11-17 08:43:32 +01:00
sdl.scm gnu: sdl-image: Add libwebp input. 2015-12-17 22:32:05 -05:00
search.scm
serialization.scm gnu: Add cereal. 2015-11-30 14:41:48 +01:00
serveez.scm
shishi.scm
skarnet.scm
skribilo.scm gnu: skribilo: Update to 0.9.3. 2016-01-13 11:13:34 +01:00
slang.scm
slim.scm
smalltalk.scm
ssh.scm gnu: openssh: Update to 7.1p2. 2016-01-15 02:46:12 -05:00
stalonetray.scm
statistics.scm gnu: r-sparsem: Add missing "gfortran" input. 2016-01-14 14:43:59 +01:00
suckless.scm
swig.scm
sxiv.scm gnu: sxiv: Update to 1.3.2. 2016-01-18 22:40:33 +03:00
synergy.scm
task-management.scm
tbb.scm
tcl.scm gnu: tcl: Produce 'tclIndex' files deterministically. 2015-11-29 22:59:28 +01:00
tcsh.scm
telephony.scm gnu: sipwitch: Update to 1.9.15. 2015-12-22 22:45:41 +02:00
terminals.scm gnu: tilda: Update to 1.3.1. 2015-12-20 09:40:56 +02:00
texinfo.scm
texlive.scm gnu: texlive: Use modify-phases syntax. 2016-01-11 10:59:29 +01:00
textutils.scm gnu: Add Pfff. 2016-01-07 21:13:35 +01:00
time.scm
tls.scm gnu: letsencrypt and acme: Update to 0.1.1. 2015-12-21 14:35:58 -05:00
tmux.scm gnu: tmux: Update to 2.1. 2015-12-14 23:23:00 -05:00
tor.scm gnu: tor: Update to 0.2.7.5. 2015-11-27 15:06:15 +01:00
tre.scm
tv.scm
unrtf.scm
upnp.scm
uucp.scm
valgrind.scm
version-control.scm gnu: Add git-annex-remote-hubic. 2016-01-17 22:37:04 +02:00
video.scm gnu: ffmpeg: Update to 2.8.5. 2016-01-21 10:30:21 -05:00
vim.scm
vpn.scm
vtk.scm
w3m.scm gnu: w3m: Enable SSL, disable broken protocols and ciphers. 2016-01-07 02:35:38 -05:00
wdiff.scm
web.scm gnu: tinyproxy: Update source URL. 2015-12-26 11:47:42 -05:00
webkit.scm gnu: webkitgtk: Update to 2.10.4. 2016-01-08 17:34:08 +08:00
weechat.scm gnu: weechat: Dynamically link against libpython2.7.so. 2015-11-29 19:17:33 +01:00
wget.scm gnu: wget: Update to 1.17.1. 2015-12-11 18:31:50 -05:00
wicd.scm
wine.scm
wm.scm gnu: Adjust formatting as recommended by 'guix lint'. 2015-11-13 23:45:55 +08:00
wordnet.scm
wv.scm
wxwidgets.scm
xdisorg.scm gnu: xlockmore: Update to 5.46. 2015-12-26 02:22:20 -05:00
xfce.scm gnu: xfce-session: Enable shutdown/reboot menu entries. 2015-11-29 20:33:35 +01:00
xfig.scm
xiph.scm gnu: libshout: Update to 2.4.1. 2016-01-20 02:12:23 +02:00
xml.scm gnu: Add xmlstarlet. 2016-01-07 16:00:00 +01:00
xnee.scm
xorg.scm gnu: xterm: Update to 322. 2016-01-08 14:12:29 +01:00
yasm.scm
yubico.scm
zile.scm
zip.scm
zsh.scm Revert "gnu: Add iftop." 2016-01-21 20:11:21 -05:00