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SRA Tools
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Building SRA-tools in Arch linux [File 'Makefile.config.linux.x86_64' is missing] error #756

Closed kbipinkumar closed 1 year ago

kbipinkumar commented 1 year ago

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

klymenko commented 1 year ago

ngs repository was moved into sra-tools. Please retry with the latest code.