environment

environment (text/plain), 12.08 KB, created by Toralf Förster on 2020-11-20 16:22:39 UTC

declare -x ABI="amd64"
declare -x ABI_MIPS=""
declare -x ABI_PPC=""
declare -x ABI_RISCV=""
declare -x ABI_S390=""
declare -x ABI_X86="64"
declare -x ADA_TARGET=""
declare -x ALSA_CARDS=""
declare -x ANGLESSHYB_DIR="/opt/cs-rosetta/ANGLESS"
declare -x ANGLESS_DIR="/opt/cs-rosetta/ANGLESS"
declare -x ANT_HOME="/usr/share/ant"
declare -x APACHE2_MODULES=""
declare -x APACHE2_MPMS=""
declare -x ARCH="amd64"
declare -x AUGUSTUS_CONFIG_PATH="/usr/share/augustus/config"
declare BDEPEND=""
declare -x BLASTDB="/usr/share/ncbi/formatdb"
declare -x BLASTMAT="/usr/share/ncbi/data"
declare -x BOOTSTRAP_USE="unicode internal-glib pkg-config split-usr python_targets_python3_7 python_targets_python2_7 multilib"
declare -x CALLIGRA_FEATURES=""
declare -x CAMERAS=""
declare -x CARGO_TERM_COLOR="never"
declare -x CBUILD="x86_64-pc-linux-gnu"
declare -x CDF_BASE="/usr"
declare -x CDF_BIN="\${CDF_BASE}/bin"
declare -x CDF_HELP="\${CDF_BASE}/lib/cdf/help"
declare -x CDF_INC="\${CDF_BASE}/include"
declare -x CDF_LIB="\${CDF_BASE}/lib"
declare -x CFLAGS="-O2 -pipe -march=native -fno-diagnostics-color "
declare -x CFLAGS_amd64="-m64"
declare -x CFLAGS_x32="-mx32"
declare -x CFLAGS_x86="-m32"
declare -x CHOST="x86_64-pc-linux-gnu"
declare -x CHOST_amd64="x86_64-pc-linux-gnu"
declare -x CHOST_x32="x86_64-pc-linux-gnux32"
declare -x CHOST_x86="i686-pc-linux-gnu"
declare -x COLLECTD_PLUGINS=""
declare -x CONCOORDBIN="/opt/concoord/bin"
declare -x CONCOORDLIB="/opt/concoord/lib"
declare -x CPU_FLAGS_ARM=""
declare -x CPU_FLAGS_PPC=""
declare -x CPU_FLAGS_X86=""
declare -x CSHYB_DIR="/opt/cs-rosetta/CS"
declare -x CS_DIR="/opt/cs-rosetta/CS"
declare -x CURL_SSL=""
declare -x CXXFLAGS="-O2 -pipe -march=native -fno-diagnostics-color "
declare -x DEFAULT_ABI="amd64"
declare -x DEFINED_PHASES=" compile install prepare"
declare DEPEND=""
declare DESCRIPTION="Parallel multi-FASTA file processing tool"
declare -x DESTTREE="/usr"
declare -x DIALIGN2_DIR="/usr/share/dialign2"
declare -x DIROPTIONS="-m0755"
declare -x DSSP="/usr/bin/dssp"
declare -x EAPI="5"
declare -x EGO_BUILD_FLAGS="-p 1"
declare -x ELIBC="glibc"
declare -x EMBOSS_ACDROOT="/usr/share/EMBOSS/acd"
declare -x EMBOSS_DATA="/usr/share/EMBOSS/data"
declare -x ENLIGHTENMENT_MODULES=""
declare -x ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
declare -- EPOCHREALTIME="1605888519.067036"
declare -- EPOCHSECONDS="1605888519"
declare -x EXEOPTIONS="-m0755"
declare -x FCFLAGS="-O2 -pipe -march=native -fno-diagnostics-color"
declare -x FETCHCOMMAND_SSH="bash -c \"x=\\\${2#ssh://} ; host=\\\${x%%/*} ; port=\\\${host##*:} ; host=\\\${host%:*} ; [[ \\\${host} = \\\${port} ]] && port= ; exec rsync --rsh=\\\"ssh \\\${port:+-p\\\${port}} \\\${3}\\\" -avP \\\"\\\${host}:/\\\${x#*/}\\\" \\\"\\\$1\\\"\" rsync \"\${DISTDIR}/\${FILE}\" \"\${URI}\" \"\${PORTAGE_SSH_OPTS}\""
declare -x FFLAGS="-O2 -pipe -march=native -fno-diagnostics-color"
declare -x FFTOOLS=""
declare -x G4ABLADATA="/usr/share/geant4/data/G4ABLA3.1"
declare -x G4ENSDFSTATEDATA="/usr/share/geant4/data/G4ENSDFSTATE2.2"
declare -x G4INCLDATA="/usr/share/geant4/data/G4INCL1.0"
declare -x G4LEDATA="/usr/share/geant4/data/G4EMLOW7.9.1"
declare -x G4LEVELGAMMADATA="/usr/share/geant4/data/PhotonEvaporation5.5"
declare -x G4NEUTRONHPDATA="/usr/share/geant4/data/G4NDL4.6"
declare -x G4PARTICLEHPDATA="/usr/share/geant4/data/G4TENDL1.3.2"
declare -x G4PARTICLEXSDATA="/usr/share/geant4/data/G4PARTICLEXS2.1"
declare -x G4PIIDATA="/usr/share/geant4/data/G4PII1.3"
declare -x G4RADIOACTIVEDATA="/usr/share/geant4/data/RadioactiveDecay5.4"
declare -x G4REALSURFACEDATA="/usr/share/geant4/data/RealSurface2.1.1"
declare -x G4SAIDXSDATA="/usr/share/geant4/data/G4SAIDDATA2.0"
declare -x GCC_COLORS=""
declare -x GCC_SPECS=""
declare -x GO19CONCURRENTCOMPILATION="0"
declare -x GOMAXPROCS="1"
declare -x GPSD_PROTOCOLS=""
declare -x GRUB_PLATFORMS=""
declare HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
declare INHERITED
declare -x INPUT_DEVICES=""
declare -x INSDESTTREE=""
declare -x INSOPTIONS="-m0644"
declare IUSE=""
declare -x IUSE_EFFECTIVE="abi_x86_64 alpha amd64 amd64-fbsd amd64-linux arm arm64 elibc_AIX elibc_Cygwin elibc_Darwin elibc_DragonFly elibc_FreeBSD elibc_HPUX elibc_Interix elibc_NetBSD elibc_OpenBSD elibc_SunOS elibc_Winnt elibc_bionic elibc_glibc elibc_mingw elibc_mintlib elibc_musl elibc_uclibc hppa ia64 kernel_AIX kernel_Darwin kernel_FreeBSD kernel_HPUX kernel_NetBSD kernel_OpenBSD kernel_SunOS kernel_Winnt kernel_freemint kernel_linux m68k m68k-mint mips ppc ppc-aix ppc-macos ppc64 ppc64-linux prefix prefix-guest prefix-stack riscv s390 sparc sparc-solaris sparc64-solaris userland_BSD userland_GNU x64-cygwin x64-macos x64-solaris x64-winnt x86 x86-cygwin x86-fbsd x86-linux x86-macos x86-solaris x86-winnt"
declare -x IUSE_IMPLICIT="abi_x86_64 prefix prefix-guest prefix-stack"
declare -x JAVAC="/etc/java-config-2/current-system-vm/bin/javac"
declare -x JAVACC_HOME="/usr/share/javacc/"
declare -x JAVA_HOME="/etc/java-config-2/current-system-vm"
declare -x JDK_HOME="/etc/java-config-2/current-system-vm"
declare -x KERNEL="linux"
declare -x KEYWORDS="~amd64 ~x86"
declare -x L10N=""
declare -x LAGAN_DIR="/usr/lib64/lagan"
declare -x LAMMPS_POTENTIALS="/usr/share/lammps/potentials"
declare -x LANG="en_US.UTF-8"
declare -x LCD_DEVICES=""
declare -x LC_MESSAGES="C"
declare -x LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0"
declare -x LDFLAGS_amd64="-m elf_x86_64"
declare -x LDFLAGS_x32="-m elf32_x86_64"
declare -x LDFLAGS_x86="-m elf_i386"
declare -x LIBDIR_amd64="lib64"
declare -x LIBDIR_x32="libx32"
declare -x LIBDIR_x86="lib"
declare -x LIBOPTIONS="-m0644"
declare -x LIBREOFFICE_EXTENSIONS=""
declare -x LICENSE="Artistic"
declare -x LIRC_DEVICES=""
declare -x LLVM_TARGETS=""
declare -x LUA_SINGLE_TARGET=""
declare -x LUA_TARGETS=""
declare -x MAKEOPTS="-j1"
declare -x MANPAGER="manpager"
declare -x MICS_DIR="//opt/mics"
declare -x MONKEYD_PLUGINS=""
declare -x MSI2LMP_LIBRARY="/usr/share/lammps/frc_files"
declare -x MULTILIB_ABIS="amd64"
declare -x MULTILIB_STRICT_DENY="64-bit.*shared object"
declare -x MULTILIB_STRICT_DIRS="/lib32 /lib /usr/lib32 /usr/lib /usr/kde/*/lib32 /usr/kde/*/lib /usr/qt/*/lib32 /usr/qt/*/lib /usr/X11R6/lib32 /usr/X11R6/lib"
declare -x MULTILIB_STRICT_EXEMPT="(perl5|gcc|binutils|eclipse-3|debug|portage|udev|systemd|clang|python-exec|llvm)"
declare -x NCBI="/etc/ncbi"
declare -x NGINX_MODULES_HTTP=""
declare -x NGINX_MODULES_MAIL=""
declare -x NGINX_MODULES_STREAM=""
declare -x NINJAFLAGS="-j1"
declare -x OCAML_COLOR="never"
declare -x OFED_DRIVERS=""
declare -x OFFICE_IMPLEMENTATION=""
declare -x OMP_DYNAMIC="FALSE"
declare -x OMP_NESTED="FALSE"
declare -x OMP_NUM_THREADS="1"
declare -x OPENMPI_FABRICS=""
declare -x OPENMPI_OFED_FEATURES=""
declare -x OPENMPI_RM=""
declare -x PATH="/usr/lib/portage/python3.7/ebuild-helpers/xattr:/usr/lib/portage/python3.7/ebuild-helpers:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/lib/llvm/11/bin:/usr/bin/cdsclient"
declare -x PAX_MARKINGS="none"
declare -x PDBHYB_DIR="/opt/cs-rosetta/PDBH"
declare -x PDBH_DIR="/opt/cs-rosetta/PDBH"
declare -x PDBH_TAB="/opt/cs-rosetta/PDBH/resolution.tab"
declare PDEPEND=""
declare -x PETSC_DIR="/usr/lib64/petsc"
declare -x PHP_TARGETS=""
declare -x PORTAGE_COMPRESSION_COMMAND="bzip2"
declare -a PORTAGE_DOCOMPRESS=([0]="/usr/share/doc" [1]="/usr/share/info" [2]="/usr/share/man")
declare -x PORTAGE_DOCOMPRESS_SIZE_LIMIT="128"
declare -a PORTAGE_DOCOMPRESS_SKIP=([0]="/usr/share/doc/pvmsx-0.1/html")
declare -a PORTAGE_DOSTRIP=([0]="/")
declare -a PORTAGE_DOSTRIP_SKIP=()
declare -x PORTAGE_TMPFS="/dev/shm"
declare -x PORT_LOGDIR="/var/log/portage"
declare -x POSTGRES_TARGETS=""
declare -x PROFILE_ONLY_VARIABLES="ARCH ELIBC IUSE_IMPLICIT KERNEL USERLAND USE_EXPAND_IMPLICIT USE_EXPAND_UNPREFIXED USE_EXPAND_VALUES_ARCH USE_EXPAND_VALUES_ELIBC USE_EXPAND_VALUES_KERNEL USE_EXPAND_VALUES_USERLAND"
declare -x PROPERTIES=""
declare -x PYTEST_ADDOPTS="--color=no"
declare -x PYTHIA8DATA="/usr/share/pythia8/xmldoc"
declare -x PYTHONDONTWRITEBYTECODE="1"
declare -x PYTHON_SINGLE_TARGET=""
declare -x PYTHON_TARGETS=""
declare -x PY_FORCE_COLOR="0"
declare -x QEMU_SOFTMMU_TARGETS=""
declare -x QEMU_USER_TARGETS=""
declare -x QRNADB="/usr/share/qrna/data"
declare RDEPEND=""
declare REPOSITORY
declare REQUIRED_USE=""
declare -x RESTRICT=""
declare -x RESUMECOMMAND_SSH="bash -c \"x=\\\${2#ssh://} ; host=\\\${x%%/*} ; port=\\\${host##*:} ; host=\\\${host%:*} ; [[ \\\${host} = \\\${port} ]] && port= ; exec rsync --rsh=\\\"ssh \\\${port:+-p\\\${port}} \\\${3}\\\" -avP \\\"\\\${host}:/\\\${x#*/}\\\" \\\"\\\$1\\\"\" rsync \"\${DISTDIR}/\${FILE}\" \"\${URI}\" \"\${PORTAGE_SSH_OPTS}\""
declare -x ROS_MESSAGES=""
declare -x RUBY_TARGETS=""
declare -x RUSTFLAGS="-C codegen-units=1"
declare -x RUST_TEST_TASKS="1"
declare -x RUST_TEST_THREADS="1"
declare -x S="/var/tmp/portage/sci-biology/pvmsx-0.1/work"
declare -x SANDBOX_DEBUG="0"
declare -x SANDBOX_DENY=""
declare -x SANDBOX_PREDICT="/var/tmp/portage/sci-biology/pvmsx-0.1/homedir:/var/cache/man:/dev/random:/proc/self/coredump_filter:/var/cache/fontconfig"
declare -x SANDBOX_READ="/:/var/tmp/portage"
declare -x SANDBOX_VERBOSE="1"
declare -x SANDBOX_WRITE=":/dev/console:/dev/fd:/dev/full:/dev/null:/dev/ptmx:/dev/pts/:/dev/pty:/dev/shm:/dev/tts:/dev/tty:/dev/vc/:/dev/zero:/proc/self/fd:/tmp/:/usr/lib32/cf:/usr/lib32/conftest:/usr/lib64/cf:/usr/lib64/conftest:/usr/lib/cf:/usr/lib/conftest:/usr/tmp/cf:/usr/tmp/conftest:/var/tmp/:/var/tmp/portage:/var/tmp/portage/sci-biology/pvmsx-0.1/homedir/.bash_history"
declare -x SANE_BACKENDS=""
declare -x SBCL_HOME="/usr/lib64/sbcl"
declare -x SBCL_SOURCE_ROOT="/usr/lib64/sbcl/src"
declare -x SHELL="/bin/bash"
declare -x SLEPC_DIR="/usr/lib64/slepc"
declare -x SLOT="0"
declare SRC_URI="
	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/pvmsx.tar.gz
	ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz"
declare -x SYMLINK_LIB="no"
declare -x TERMINFO="/etc/terminfo"
declare -x TWISTED_DISABLE_WRITING_OF_PLUGIN_CACHE="1"
declare -x USE="abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU"
declare -x USERLAND="GNU"
declare -x USE_EXPAND_IMPLICIT="ARCH ELIBC KERNEL USERLAND"
declare -x USE_EXPAND_UNPREFIXED="ARCH"
declare -x USE_EXPAND_VALUES_ARCH="alpha amd64 amd64-fbsd amd64-linux arm arm64 hppa ia64 m68k m68k-mint mips ppc ppc64 ppc64-linux ppc-aix ppc-macos riscv s390 sparc sparc64-solaris sparc-solaris x64-cygwin x64-macos x64-solaris x64-winnt x86 x86-cygwin x86-fbsd x86-linux x86-macos x86-solaris x86-winnt"
declare -x USE_EXPAND_VALUES_ELIBC="AIX bionic Cygwin Darwin DragonFly FreeBSD glibc HPUX Interix mingw mintlib musl NetBSD OpenBSD SunOS uclibc Winnt"
declare -x USE_EXPAND_VALUES_KERNEL="AIX Darwin FreeBSD freemint HPUX linux NetBSD OpenBSD SunOS Winnt"
declare -x USE_EXPAND_VALUES_USERLAND="BSD GNU"
declare -x UWSGI_PLUGINS=""
declare -x VIDEO_CARDS=""
declare -x VOICEMAIL_STORAGE=""
declare -x XEHELPURL="/usr/share/doc/xephem-3.7.7/html/xephem.html"
declare -x XFCE_PLUGINS=""
declare -x XTABLES_ADDONS=""
declare -x _E_DOCDESTTREE_=""
declare -x _E_EXEDESTTREE_=""
__eapi6_src_install () 
{ 
    if [[ -f Makefile || -f GNUmakefile || -f makefile ]]; then
        emake DESTDIR="${D}" install;
    fi;
    einstalldocs
}
__eapi6_src_prepare () 
{ 
    if ___is_indexed_array_var PATCHES; then
        [[ ${#PATCHES[@]} -gt 0 ]] && eapply "${PATCHES[@]}";
    else
        if [[ -n ${PATCHES} ]]; then
            eapply ${PATCHES};
        fi;
    fi;
    eapply_user
}
pkg_nofetch () 
{ 
    default
}
src_compile () 
{ 
    default
}
src_configure () 
{ 
    default
}
src_install () 
{ 
    dobin ${PN};
    newdoc README README.${PN}
}
src_prepare () 
{ 
    sed -e 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' -i "${S}"/Makefile || die "Failed to run sed";
    sed -e 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' -i "${S}"/Makefile || die;
    sed -e "s#-I-#-iquote#" -i "${S}"/Makefile || die;
    ln -s ../cdbfasta/gcl . || die "Cannot make a softlink"
}
src_test () 
{ 
    default
}
src_unpack () 
{ 
    default
}