i am trying to build and package sra-tools for arch linux.
from your wiki, my understanding is that i need to download and extract source tarballs for ncbi-vdb and sra-tools to same folder and then run ./configure and make in folder of ncbi-vdb and sra-tools in the aforementioned order followed by make install
in archlinux this process can be automated in `PKGBUILD' script which is essentially a bash script like this
build(){
cd "ncbi-vdb-3.0.2"
./configure \
--prefix="$pkgdir/usr/"
make
cd ..
cd "sra-tools-3.0.2"
/configure \
--prefix="$pkgdir/usr/"
make
cd ..
}
the script creates aforementioned ncbi-vdb and sra-tools folders in the /build/sra-tools/src location
now the script runs fine and builds ncbi-vdb as shown in output below
[ 99%] Built target ncbi-vdb
[ 99%] Linking C shared library /build/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib/libncbi-vdb.so
[ 99%] Built target ncbi-vdb-shared
[ 99%] Linking C static library /build/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib/libncbi-wvdb.a
[ 99%] Built target ncbi-wvdb
[100%] Linking C shared library /build/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib/libncbi-wvdb.so
[100%] Built target ncbi-wvdb-shared
but when is start running ./configure in `sra-tools-3.0.2' tools directory i am getting following error
CONFIGURING ngs-sdk
Unknown option: with-hdf5
configure: error at konfigure.perl line 109.
CONFIGURING ngs-java
Unknown option: with-hdf5
configure: error at konfigure.perl line 109.
CONFIGURING ngs-python
Unknown option: with-hdf5
configure: error at konfigure.perl line 109.
make[1]: Entering directory '/build/sra-tools/src/ngs-3.0.1/ngs-sdk'
*** File 'Makefile.config.linux.x86_64' is missing. Please run ./configure
make[1]: *** [/build/sra-tools/src/ngs-3.0.1/ngs-sdk/Makefile.rules:72: Makefile.config.linux.x86_64] Error 1
make[1]: Leaving directory '/build/sra-tools/src/ngs-3.0.1/ngs-sdk'
make: *** [Makefile:54: ngs-sdk] Error 2
any idea regarding what am i doing wrong? i dont remember even passing this Unknown option: with-hdf5 option as well
i am trying to build and package sra-tools for arch linux.
from your wiki, my understanding is that i need to download and extract source tarballs for
ncbi-vdb
andsra-tools
to same folder and then run./configure
andmake
in folder ofncbi-vdb
andsra-tools
in the aforementioned order followed by make installin archlinux this process can be automated in `PKGBUILD' script which is essentially a bash script like this
the script creates aforementioned
ncbi-vdb
andsra-tools
folders in the/build/sra-tools/src
locationnow the script runs fine and builds ncbi-vdb as shown in output below
but when is start running
./configure
in `sra-tools-3.0.2' tools directory i am getting following errorany idea regarding what am i doing wrong? i dont remember even passing this
Unknown option: with-hdf5
option as well