[PATCH 0/4] Add sra-tools.

[Ricardo Wurmus]

Hi Guix,

this patch set adds the sra tools (a collection containing the commonly
encountered "fastq-dump") and its dependencies.

The NCBI stuff uses a frustrating custom configuration script written in
Perl and I had to learn more about how it works and what assumptions it
makes than I hoped for.

More significant changes had to be made to the build of both ncbi-vdb
and sra-tools, because sra-tools expects the sources and the raw build
output of ncbi-vdb to lie in some directory.  It would not build against
an installed version of ncbi-vdb due to missing libraries and missing
includes.

As both of these projects have been split from the same repository in
the recent past and are so closely coupled I took the liberty to let
ncbi-vdb install more headers and more libraries, so that at the time
sra-tools is built we don't need to rebuild ncbi-vdb just to get at the
includes and interface libraries.  The phases do not look pretty but
they are as clean as I could make them.

I had to remove libxml2 from the inputs to sra-tools, resulting in a
failure to build a couple of loader tools.  The reason for this is that
I encountered linker problems like these:


~~~~~~~~~~
...
gcc -static-libstdc++ -static-libgcc -o 
/buildtmp/nix-build-sra-tools-2.4.5-5.drv-4/sra-tools-2.4.5-5/build/sra-tools/linux/gcc/x86_64/rel/bin/fastq-load.2.4.5
 -DNDEBUG -m64 -L/gnu/store/pjjpcai7ckqlric0p0xdrzjsifdx1d44-hdf5-1.8.12/lib 
-L/gnu/store/3x1qwishrgvsvaddhv2238s27jcg60wp-libxml2-2.9.0/lib 
-L/gnu/store/xbvqikb6y02zqpvac876sxy4ci937spd-file-5.22/lib 
-L/gnu/store/35gqycjy0ih7wrjadzhvixya0a905sf5-fuse-2.9.3/lib pstring.o 
common-xml.o experiment-xml.o run-xml.o loader-file.o loader-fmt.o sra-writer.o 
loader.o writer-illumina.o writer-454.o writer-ion-torrent.o fastq-fmt.o 
-L/buildtmp/nix-build-sra-tools-2.4.5-5.drv-4/sra-tools-2.4.5-5/build/sra-tools/linux/gcc/x86_64/rel/lib
 
-L/buildtmp/nix-build-sra-tools-2.4.5-5.drv-4/sra-tools-2.4.5-5/build/sra-tools/linux/gcc/x86_64/rel/ilib
 -L/gnu/store/xldsqaj0cw6v89karyx1izhhmxihpmb1-ngs-sdk-1.1.0/lib64 
-L/gnu/store/fjpl0vm87dzn3hpvqaca625bq8hv1mha-ncbi-vdb-2.4.5-5/ilib 
-Wl,-Bstatic -lkapp -lload -lncbi-wvdb -lkxfs -lkxml -Wl,-Bdynamic -ldl 
-lpthread -Wl,-Bstatic 
-L/gnu/store/3x1qwishrgvsvaddhv2238s27jcg60wp-libxml2-2.9.0/lib -lxml2 
-Wl,-Bdynamic -lm
/gnu/store/3x1makeqwishrgvsvaddhv2238s27jcg60wp-libxml2-2.9.0/lib/libxml2.a(xmlIO.o):
 In function `xmlGzfileOpenW':
(.text+0x2c9): undefined reference to `gzdopen'
/gnu/store/3x1qwishrgvsvaddhv2238s27jcg60wp-libxml2-2.9.0/lib/libxml2.a(xmlIO.o):
 In function `xmlGzfileOpenW':
(.text+0x2fe): undefined reference to `gzopen64'
/gnu/store/3x1qwishrgvsvaddhv2238s27jcg60wp-libxml2-2.9.0/lib/libxml2.a(xmlIO.o):
 In function `xmlGzfileClose':
(.text+0xe85): undefined reference to `gzclose'
/gnu/store/3x1qwishrgvsvaddhv2238s27jcg60wp-libxml2-2.9.0/lib/libxml2.a(xmlIO.o):
 In function `xmlGzfileRead':
(.text+0xeb5): undefined reference to `gzread'
/gnu/store/3x1qwishrgvsvaddhv2238s27jcg60wp-libxml2-2.9.0/lib/libxml2.a(xmlIO.o):
 In function `xmlGzfileWrite':
(.text+0x1095): undefined reference to `gzwrite'
/gnu/store/3x1qwishrgvsvaddhv2238s27jcg60wp-libxml2-2.9.0/lib/libxml2.a(xmlIO.o):
 In function `__xmlParserInputBufferCreateFilename':
(.text+0x1d82): undefined reference to `gzdirect'
/gnu/store/3x1qwishrgvsvaddhv2238s27jcg60wp-libxml2-2.9.0/lib/libxml2.a(xmlIO.o):
 In function `xmlGzfileOpen_real':
(.text+0x171f): undefined reference to `gzdopen'
/gnu/store/3x1qwishrgvsvaddhv2238s27jcg60wp-libxml2-2.9.0/lib/libxml2.a(xmlIO.o):
 In function `xmlGzfileOpen_real':
(.text+0x175d): undefined reference to `gzopen64'
/gnu/store/3x1qwishrgvsvaddhv2238s27jcg60wp-libxml2-2.9.0/lib/libxml2.a(xzlib.o):
 In function `xz_decomp':
(.text+0x5a4): undefined reference to `lzma_code'
/gnu/store/3x1qwishrgvsvaddhv2238s27jcg60wp-libxml2-2.9.0/lib/libxml2.a(xzlib.o):
 In function `xz_make':
(.text+0x983): undefined reference to `lzma_properties_decode'
/gnu/store/3x1qwishrgvsvaddhv2238s27jcg60wp-libxml2-2.9.0/lib/libxml2.a(xzlib.o):
 In function `xz_make':
(.text+0xbb8): undefined reference to `lzma_auto_decoder'
/gnu/store/3x1qwishrgvsvaddhv2238s27jcg60wp-libxml2-2.9.0/lib/libxml2.a(xzlib.o):
 In function `__libxml2_xzclose':
(.text+0x1605): undefined reference to `lzma_end'
collect2: error: ld returned 1 exit status