69656bf0d7
SRA tools is a toolkit for using data in the INSDC Sequence Read Archives. SRAs operated by International Nucleotide Sequence Database Collaboration houses sequence reads and alignments generated by "next-gen" sequencers. This port is a bit convoluted due to the fact that the sra-tools build requires access to the ncbi-vdb source tree. Hence, ncbi-vdb is treated as a submodule here rather than a separate library port. We are working with upstream with hope for long-term improvements.
158 lines
3.1 KiB
Bash
Executable file
158 lines
3.1 KiB
Bash
Executable file
#!/usr/local/bin/bash
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# ===========================================================================
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#
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# PUBLIC DOMAIN NOTICE
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# National Center for Biotechnology Information
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#
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# This software/database is a "United States Government Work" under the
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# terms of the United States Copyright Act. It was written as part of
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# the author's official duties as a United States Government employee and
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# thus cannot be copyrighted. This software/database is freely available
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# to the public for use. The National Library of Medicine and the U.S.
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# Government have not placed any restriction on its use or reproduction.
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#
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# Although all reasonable efforts have been taken to ensure the accuracy
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# and reliability of the software and data, the NLM and the U.S.
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# Government do not and cannot warrant the performance or results that
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# may be obtained by using this software or data. The NLM and the U.S.
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# Government disclaim all warranties, express or implied, including
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# warranties of performance, merchantability or fitness for any particular
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# purpose.
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#
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# Please cite the author in any work or product based on this material.
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#
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# ===========================================================================
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# script name
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SELF_NAME="$(basename $0)"
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# parameters
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LD="$1"
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ARCH="$2"
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BUILD="$3"
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shift 3
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SRCDIR="$1"
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BINDIR="$2"
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OUTDIR="$3"
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TARG="$4"
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NAME="$5"
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DBGAP="$6"
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shift 6
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VERS="$1"
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VERSFILE="$2"
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DEPFILE="$3"
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shift 3
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MODE="$1"
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SCMFLAGS="$2"
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LDFLAGS="$3"
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shift 3
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LDIRS="$1"
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XDIRS="$2"
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shift 2
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OBJS="$1"
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LIBS="$2"
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# decode MODE
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STATIC=$(expr $MODE % 2)
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MODE=$(expr $MODE / 2)
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DYLD=$(expr $MODE % 2)
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MODE=$(expr $MODE / 2)
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KPROC=$(expr $MODE % 2)
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MODE=$(expr $MODE / 2)
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THREADS=$(expr $MODE % 2)
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MODE=$(expr $MODE / 2)
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HAVE_M=$(expr $MODE % 2)
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MODE=$(expr $MODE / 2)
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HAVE_XML=$(expr $MODE % 2)
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# decode SCMFLAGS
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CHECKSUM=$(expr $SCMFLAGS % 2)
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STATICSYSLIBS=$(expr $SCMFLAGS / 2)
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# return parameter for find-lib
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LIBPATH=''
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# initial command state
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CMD=''
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LD_STATIC_STATE=0
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LD_ALL_STATE=0
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# for breaking out version
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set-vers ()
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{
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MAJ=$1
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MIN=$2
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REL=$3
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}
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# for locating libraries
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find-lib ()
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{
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_lib="lib$1"
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_dirs="$2"
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LIBPATH=''
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while [ "$_dirs" != "" ]
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do
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_dir="${_dirs%%:*}"
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if [ "$_dir" != "" ]
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then
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if [ -e "$_dir/$_lib" ]
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then
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while [ -L "$_dir/$_lib" ]
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do
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_lib=$(readlink -n "$_dir/$_lib")
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done
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LIBPATH="$_dir/$_lib"
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break;
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fi
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fi
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_dirs="${_dirs#$_dir}"
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_dirs="${_dirs#:}"
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done
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}
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# setting state
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load-static ()
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{
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if [ $LD_STATIC_STATE -eq 0 ]
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then
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CMD="$CMD $LD_STATIC"
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LD_STATIC_STATE=1
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fi
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}
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load-dynamic ()
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{
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if [ $LD_STATIC_STATE -eq 1 ]
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then
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CMD="$CMD $LD_DYNAMIC"
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LD_STATIC_STATE=0
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fi
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}
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load-all-symbols ()
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{
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if [ $LD_ALL_STATE -eq 0 ]
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then
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CMD="$CMD $LD_ALL_SYMBOLS"
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LD_ALL_STATE=1
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fi
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}
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load-ref-symbols ()
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{
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if [ $LD_ALL_STATE -eq 1 ]
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then
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CMD="$CMD $LD_REF_SYMBOLS"
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LD_ALL_STATE=0
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fi
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}
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