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6518 Commits

Author SHA1 Message Date
Ricardo Wurmus dbf4ed7c91 gnu: Add subread. 
* gnu/packages/bioinformatics.scm (subread): New variable.
 2015-04-21 10:46:23 +02:00
Ludovic Courtès 44fd6ef137 ui: Add 'symlink' replacement with better error reporting. 
* guix/ui.scm (symlink): New procedure.
 2015-04-20 22:37:20 +02:00
Ludovic Courtès 3392ce5d60 system: Make /gnu/store a read-only bind mount by default. 
* gnu/system/file-systems.scm (%immutable-store): New variable.
  (%base-file-systems): Add it.
* doc/guix.texi (File Systems): Document it.
 2015-04-20 22:21:51 +02:00
Ludovic Courtès b86fee7848 file-systems: Use a second 'mount' call for read-only bind mounts. 
* gnu/build/file-systems.scm (MS_REMOUNT): New constant.
  (mount-file-system): Add 'flags' local variable.   When FLAGS has
  MS_BIND & MS_RDONLY, call 'mount' with MS_REMOUNT.
* gnu/services/base.scm (file-system-service) <start>: Likewise.
 2015-04-20 22:16:13 +02:00
Ludovic Courtès 38cf2ba084 gnu: Remove all #:select from (gnu packages ...) modules. 
This works around Guile bug <http://bugs.gnu.org/15540>.
Reported by Andreas Enge <andreas@enge.fr>.

* gnu/packages/engineering.scm: Don't #:select from (gnu packages ...).
* gnu/packages/gcc.scm: Likewise.
* gnu/packages/package-management.scm: Likewise.
* gnu/packages/photo.scm: Likewise.
* gnu/packages/pulseaudio.scm: Likewise.
* gnu/packages/moe.scm: Likewise, and #:select from (guix licenses)
  instead.
 2015-04-20 15:50:59 +02:00
Ludovic Courtès f73286345e gexp: Add printers for <gexp-input> and <gexp-output>. 
* guix/gexp.scm (write-gexp-input, write-gexp-output): New procedures.
  (<gexp-input>, <gexp-output>): Use them as printers.
 2015-04-20 15:41:41 +02:00
Ludovic Courtès c568191a93 profiles: Create a CA certificate bundle only when it would be non-empty. 
* guix/profiles.scm (ca-certificate-bundle): Create
  $output/etc/ssl/certs if and only if CA-FILES is non-empty.
 2015-04-20 15:41:41 +02:00
Ricardo Wurmus 51c649992e gnu: Add sra-tools. 
* gnu/packages/bioinformatics.scm (sra-tools): New variable.
 2015-04-20 15:29:17 +02:00
Ricardo Wurmus 75dd242480 gnu: Add NCBI VDB. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): New variable.
 2015-04-20 15:29:17 +02:00
Ricardo Wurmus 2651a5e695 gnu: Add NGS Java bindings. 
* gnu/packages/bioinformatics.scm (ngs-java): New variable.
 2015-04-20 15:29:16 +02:00
Ricardo Wurmus 282c5087b4 gnu: Add NGS SDK. 
* gnu/packages/bioinformatics.scm (ngs-sdk): New variable.
 2015-04-20 15:28:58 +02:00
Ricardo Wurmus 85c37e29a4 gnu: Add Biopython. 
* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): New
  variables.
 2015-04-20 15:23:23 +02:00
Eric Bavier 40b084a326 gnu: Adjust latest perl modules to new 'modify-phases' syntax. 
* gnu/packages/compression.scm (perl-compress-raw-zlib)[arguments]:
  Add missing quotes, as needed since commit f8503e2.
* gnu/packages/perl.scm (perl-ipc-run)[arguments]: Likewise.
* gnu/packages/xml.scm (perl-xml-sax)[arguments]: Likewise.
 2015-04-19 21:39:32 -05:00
宋文武 61c21ad319 gnu: Add WebKitGTK+. 
* gnu/packages/webkit.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
 2015-04-20 10:34:24 +08:00
Eric Bavier 97b05abe6d gnu: Add JSON-Any. 
* gnu/packages/perl.scm (perl-json-any): New variable.
 2015-04-19 19:48:52 -05:00
Eric Bavier 47945cf353 import: cpan: Fix license string for Artistic license. 
* guix/import/cpan.scm (string->license): Remove extraneous "_0"
  suffix for Artistics licenses.
 2015-04-19 19:48:52 -05:00
Eric Bavier ae6904dc0b gnu: nix: Propagate perl inputs. 
* gnu/packages/package-management.scm (nix)[inputs]: Move
  perl-www-curl, perl-dbi, perl-dbd-sqlite to...
  [propagated-inputs]: ...this new field
 2015-04-19 19:48:52 -05:00
Eric Bavier 8ac84f230c gnu: Add Sys-Hostname-Long. 
* gnu/packages/perl.scm (perl-sys-hostname-long): New variable.
 2015-04-19 19:48:52 -05:00
Eric Bavier 10ef803e7d gnu: Add Text-Table. 
* gnu/packages/perl.scm (perl-text-table): New variable.
 2015-04-19 19:48:52 -05:00
Eric Bavier 7ae9557181 gnu: Add Text-Aligner. 
* gnu/packages/perl.scm (perl-text-aligner): New variable.
 2015-04-19 19:48:52 -05:00
Eric Bavier f21671f469 gnu: Add Set-Scalar. 
* gnu/packages/perl.scm (perl-set-scalar): New variable.
 2015-04-19 19:48:52 -05:00
Eric Bavier b4dcb026d6 gnu: Add SQL-SplitStatement. 
* gnu/packages/databases.scm (perl-sql-splitstatement): New variable.
 2015-04-19 19:48:52 -05:00
Eric Bavier 718c89c1a1 gnu: Add SQL-Tokenizer. 
* gnu/packages/databases.scm (perl-sql-tokenizer): New variable.
 2015-04-19 19:48:52 -05:00
Eric Bavier 8ce2312875 gnu: Add Perl Readonly. 
* gnu/packages/perl.scm (perl-readonly): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier 38e62c81ee gnu: Add Perl Net-Amazon-S3. 
* gnu/packages/patches/perl-net-amazon-s3-moose-warning.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/web.scm (perl-net-amazon-s3): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier 3dd6bee1f2 gnu: Add XML-LibXML. 
* gnu/packages/xml.scm (perl-xml-libxml): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier 18b8bbb304 gnu: Add XML-SAX; 
* gnu/packages/xml.scm (perl-xml-sax): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier 1ed6d5bc86 gnu: Add XML-SAX-Base. 
* gnu/packages/xml.scm (perl-xml-sax-base): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier b715dbac7b gnu: Add XML-NamespaceSupport. 
* gnu/packages/xml.scm (perl-xml-namespacesupport): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier 0955342bf7 gnu: Add Term-ProgressBar-Simple. 
* gnu/packages/perl.scm (perl-term-progressbar-simple): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier 0d54bd259c gnu: Add Term-ProgressBar-Quiet. 
* gnu/packages/perl.scm (perl-term-progressbar-quiet): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier 4dbac597eb gnu: Add Test-MockObject. 
* gnu/packages/perl.scm (perl-test-mockobject): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier 7332618df3 gnu: Add UNIVERSAL-isa. 
* gnu/packages/perl.scm (perl-universal-isa): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier f9671ab689 gnu: Add UNIVERSAL-can. 
* gnu/packages/perl.scm (perl-universal-can): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier cc307bda85 gnu: Add Term-ProgressBar. 
* gnu/packages/perl.scm (perl-term-progressbar): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier 70fe0008f7 gnu: Add TermReadKey. 
* gnu/packages/perl.scm (perl-term-readkey): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier cd718b8201 gnu: Add Class-MethodMaker. 
* gnu/packages/perl.scm (perl-class-methodmaker): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier 56da2a1abd gnu: Add IO-Interactive. 
* gnu/packages/perl.scm (perl-io-interactive): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier 257fa40b23 gnu: Add Term-Encoding. 
* gnu/packages/perl.scm (perl-term-encoding): New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier d2401db9ff gnu: Add MooseX-Types-DateTime-MoreCoercions. 
* gnu/packages/perl.scm (perl-moosex-types-datetime-morecoercions):
  New variable.
 2015-04-19 19:48:51 -05:00
Eric Bavier 4f43da182b gnu: Add Time-Duration-Parse. 
* gnu/packages/perl.scm (perl-time-duration-parse): New variable.
 2015-04-19 19:48:50 -05:00
Eric Bavier a15145d93b gnu: Add Time-Duration. 
* gnu/packages/perl.scm (perl-time-duration): New variable.
 2015-04-19 19:48:50 -05:00
Eric Bavier bbe81cc0dd gnu: Add Test-Pod-Coverage. 
* gnu/packages/perl.scm (perl-test-pod-coverage): New variable.
 2015-04-19 19:48:50 -05:00
Eric Bavier 29fda459a6 gnu: Add Pod-Coverage. 
* gnu/packages/perl.scm (perl-pod-coverage): New variable.
 2015-04-19 19:48:50 -05:00
Eric Bavier 7300092693 gnu: Add Devel-Symdump. 
* gnu/packages/perl.scm (perl-devel-symdump): New variable.
 2015-04-19 19:48:50 -05:00
Eric Bavier 3e7a86cdc5 gnu: Add MooseX-Types-DateTime. 
* gnu/packages/perl.scm (perl-moosex-types-datetime): New variable.
 2015-04-19 19:48:50 -05:00
Eric Bavier ef96132220 gnu: Add DateTimeX-Easy. 
* gnu/packages/perl.scm (perl-datetimex-easy): New variable.
 2015-04-19 19:48:50 -05:00
Eric Bavier 69d2261f77 gnu: Add DateTime-Format-Natural. 
* gnu/packages/perl.scm (perl-datetime-format-natural): New variable.
 2015-04-19 19:48:50 -05:00
Eric Bavier 55069500a2 gnu: Add Module-Util. 
* gnu/packages/perl.scm (perl-module-util): New variable.
 2015-04-19 19:48:50 -05:00
Eric Bavier 59f423214e gnu: Add Date-Calc. 
* gnu/packages/perl.scm (perl-date-calc, perl-date-calc-xs): New
  variables.
 2015-04-19 19:48:50 -05:00