gnu: gcc: Add a RUNPATH to libstdc++.so so that it finds libgcc_s.so.

Fixes <http://bugs.gnu.org/20358>.
Reported by 宋文武 <iyzsong@gmail.com>.

* gnu/packages/gcc.scm (gcc-4.7)[arguments]: Add 'substitute*' form for
  "libstdc++-v3/src/Makefile.in".

gnu: commencement: Remove unneeded configure flag for bootstrap gettext.

* gnu/packages/commencement.scm (gettext-boot0): Remove unneeded
  --disable-threads.

gnu: perl: Fix Module::Pluggable for symlink forests.

* gnu/packages/patches/perl-module-pluggable-search.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/perl.scm (perl)[source]: Add patch.

gnu: tzdata: Update to 2015c.

* gnu/packages/base.scm (tzdata): Update to 2015c.

gnu: glibc: Add dependency on Gettext, to install the message catalogs.

This fixes a bug whereby the libc.mo files were not installed, and thus
translations of libc's messages were not available.

* gnu/packages/commencement.scm (gettext-boot0): New variable.
  (glibc-final)[native-inputs]: New field.
* gnu/packages/base.scm (glibc)[native-inputs]: Add GNU-GETTEXT.

gnu: libltdl: Remove unneeded patch.

* gnu/packages/autotools.scm (libltdl)[source]: Remove 'patches'.

gnu: ld-wrapper: Ignore the .so argument following '-dynamic-linker'.

Reported at <http://bugs.gnu.org/20102>.

* gnu/packages/ld-wrapper.in (library-files-linked): Rename 'path+files'
  to 'path+files+args'.  Thread the reverse list of previous arguments.
  Add case for when the previous argument is "-dynamic-linker".

gnu: ld-wrapper: Add debugging info.

* gnu/packages/ld-wrapper.in (ld-wrapper): Add "libraries linked"
  debugging statement.

gnu: Rename ld-wrapper2 to ld-wrapper.

* gnu/packages/ld-wrapper2.in: Rename to...
* gnu/packages/ld-wrapper.in: ... this.
* gnu-system.am (MISC_DISTRO_FILES): Remove ld-wrapper2.in.
* gnu/packages/commencement.scm (fixed-ld-wrapper): Remove.
  (gcc-toolchain): Restore pre-77db91ad inputs.

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.

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.

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.

gnu: Add sra-tools.

* gnu/packages/bioinformatics.scm (sra-tools): New variable.

gnu: Add NCBI VDB.

* gnu/packages/bioinformatics.scm (ncbi-vdb): New variable.

gnu: Add NGS Java bindings.

* gnu/packages/bioinformatics.scm (ngs-java): New variable.

gnu: Add NGS SDK.

* gnu/packages/bioinformatics.scm (ngs-sdk): New variable.

gnu: Add Biopython.

* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): New
  variables.

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.

gnu: Add WebKitGTK+.

* gnu/packages/webkit.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.

gnu: Add JSON-Any.

* gnu/packages/perl.scm (perl-json-any): New variable.