diff x/build_env_setup.sh @ 133:cec274db51c0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7d28252954cae9f8db5f8a85d8f29cb2865b504b-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/x/build_env_setup.sh	Fri Oct 18 11:57:55 2024 +0000
@@ -0,0 +1,396 @@
+export CONDA_BUILD="1"
+export PYTHONNOUSERSITE="1"
+export CONDA_DEFAULT_ENV="/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881"
+export ARCH="64"
+export PREFIX="/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881"
+export BUILD_PREFIX="/opt/conda/conda-bld/jbrowse2_1726856947541/_build_env"
+export SYS_PREFIX="/opt/conda"
+export SYS_PYTHON="/opt/conda/bin/python"
+export SUBDIR="linux-64"
+export build_platform="linux-64"
+export SRC_DIR="/opt/conda/conda-bld/jbrowse2_1726856947541/work"
+export ROOT="/opt/conda"
+export CONDA_PY="312"
+export PY3K="1"
+export PY_VER="3.12"
+export STDLIB_DIR="/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881/lib/python3.12"
+export SP_DIR="/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881/lib/python3.12/site-packages"
+export NPY_VER="1.26"
+export CONDA_NPY="126"
+export NPY_DISTUTILS_APPEND_FLAGS="1"
+export PERL_VER="5.32"
+export CONDA_PERL="5.32"
+export LUA_VER="5"
+export CONDA_LUA="5"
+export R_VER="4.3.*"
+export CONDA_R="4.3.*"
+export PKG_NAME="jbrowse2"
+export PKG_VERSION="2.15.4"
+export PKG_BUILDNUM="0"
+export PKG_BUILD_STRING="placeholder"
+export PKG_HASH="1234567"
+export RECIPE_DIR="/opt/recipe"
+export CPU_COUNT="2"
+export LANG="C.UTF-8"
+export SHLIB_EXT=".so"
+export PATH="/opt/conda/conda-bld/jbrowse2_1726856947541/_build_env/bin:/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881/bin:/opt/conda/bin:/opt/conda/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/conda/bin"
+export HOME="/home/conda"
+export PKG_CONFIG_PATH="/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881/lib/pkgconfig"
+export CMAKE_GENERATOR="Unix Makefiles"
+export LD_RUN_PATH="/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881/lib"
+export BUILD="x86_64-conda_cos6-linux-gnu"
+export zip_keys="[['c_compiler_version', 'cxx_compiler_version', 'fortran_compiler_version'], ['arrow_cpp', 'libarrow', 'libarrow_all'], ['python', 'numpy', 'python_impl'], ['c_stdlib_version', 'cdt_name']]"
+export pin_run_as_build="OrderedDict([('python', {'min_pin': 'x.x', 'max_pin': 'x.x'}), ('r-base', {'max_pin': 'x.x', 'min_pin': 'x.x'}), ('flann', {'max_pin': 'x.x.x'}), ('graphviz', {'max_pin': 'x'}), ('libsvm', {'max_pin': 'x'}), ('netcdf-cxx4', {'max_pin': 'x.x'}), ('occt', {'max_pin': 'x.x'}), ('poppler', {'max_pin': 'x.x'}), ('vlfeat', {'max_pin': 'x.x.x'})])"
+export extend_keys="{'ignore_version', 'pin_run_as_build', 'extend_keys', 'ignore_build_only_deps'}"
+export ignore_build_only_deps="{'python', 'numpy'}"
+export libyarp="3.9.0"
+export libintervalxt="3"
+export tk="8.6"
+export libmatio="1.5.26"
+export qt="5.15"
+export coin_or_cgl="0.60"
+export coincbc="2.10"
+export pixman="0"
+export libhugetlbfs="2"
+export libopencv="4.9.0"
+export ccr="1.3"
+export superlu_dist="8"
+export libsoup="3"
+export pyqtwebengine="5.15"
+export hdf4="4.2.15"
+export gst_plugins_base="1.22"
+export eclib="20231211"
+export google_cloud_cpp_common="0.25.0"
+export dcap="2.47"
+export slepc4py="3.21"
+export scotch="7.0.4"
+export snappy="1.2"
+export suitesparse="5"
+export libblitz="1.0.2"
+export libabseil_static="20220623.0"
+export libflatsurf="3"
+export pulseaudio="17.0"
+export libcblas="3.9 *netlib"
+export libgoogle_cloud_dlp_devel="2.24"
+export rocksdb="9.1"
+export _libgcc_mutex="0.1 conda_forge"
+export gnuradio_core="3.10.10"
+export librdkafka="2.4"
+export libdap4="3.20.6"
+export aws_c_auth="0.7.22"
+export channel_targets="bioconda main"
+export libhwloc="2.10.0"
+export pyqt="5.15"
+export cpu_optimization_target="nocona"
+export assimp="5.3.1"
+export mpfr="4"
+export pcre2="10.43"
+export gsl="2.7"
+export ptscotch="7.0.4"
+export xrootd="5"
+export arpack="3.8"
+export cxx_compiler="gxx"
+export sdl2_net="2"
+export target_goos="linux"
+export elfutils="0.191"
+export libhwy="1.1"
+export uhd="4.6.0"
+export petsc="3.21"
+export pulseaudio_daemon="17.0"
+export libeantic="2"
+export libopentelemetry_cpp="1.15"
+export bamtools="2.5.2"
+export openblas="0.3.*"
+export icu="73"
+export libiio="0"
+export x264="1!164.*"
+export mpich="4"
+export pybind11_abi="4"
+export nettle="3.9"
+export libwebp_base="1"
+export abseil_cpp="20220623.0"
+export thrift_cpp="0.18.1"
+export openmpi="4"
+export coin_or_cbc="2.10"
+export openslide="4"
+export libscotch="7.0.4"
+export sdl2_mixer="2"
+export fontconfig="2"
+export libgoogle_cloud_oauth2_devel="2.24"
+export grpc_cpp="1.52"
+export libmatio_cpp="0.2.5"
+export libboost_python_devel="1.82"
+export openh264="2.4.1"
+export pcre="8"
+export vlfeat="0.9.21"
+export mumps_seq="5.7.1"
+export gct="6.2.1705709074"
+export openssl="3"
+export dbus="1"
+export googleapis_cpp="0.10"
+export xz="5"
+export coin_or_clp="1.17"
+export libcurl="8"
+export aws_checksums="0.1.18"
+export libtensorflow="2.15"
+export libidn2="2"
+export aws_c_common="0.9.19"
+export google_cloud_cpp="2.24"
+export libsqlite="3"
+export libthrift="0.20.0"
+export ucx="1.16.0"
+export re2="2023.09.01"
+export c_compiler="gcc"
+export zlib="1.2"
+export gnutls="3.7"
+export aws_sdk_cpp="1.11.267"
+export mpg123="1.32"
+export libevent="2.1.12"
+export go_compiler="go-nocgo"
+export libarchive="3.7"
+export msgpack_c="6"
+export ntl="11.4.3"
+export davix="0.8"
+export libev="4.33"
+export ruby="2.6"
+export glog="0.6"
+export libopenvino_dev="2024.1.0"
+export exiv2="0.28"
+export libpng="1.6"
+export ncurses="6"
+export lz4_c="1.9.3"
+export libzip="1"
+export sqlite="3"
+export postgresql_plpython="16"
+export libprotobuf="4.25.3"
+export gdal="3.8"
+export libcint="5.5"
+export geos="3.12.1"
+export qt6_main="6.7"
+export libgdal="3.8"
+export occt="7.7.2"
+export lcms2="2"
+export librsvg="2"
+export libgoogle_cloud_bigquery_devel="2.24"
+export libffi="3.4"
+export tinyxml2="10"
+export zstd="1.5"
+export fmt="10"
+export libframel="8.41"
+export libgoogle_cloud_dialogflow_cx_devel="2.24"
+export jsoncpp="1.9.5"
+export libgoogle_cloud_dialogflow_es_devel="2.24"
+export target_platform="linux-64"
+export gflags="2.2"
+export aws_c_sdkutils="0.1.16"
+export aws_c_http="0.8.1"
+export netcdf_cxx4="4.3"
+export libjpeg_turbo="3"
+export sox="14.4.2"
+export VERBOSE_CM="VERBOSE=1"
+export jasper="4"
+export coin_or_osi="0.108"
+export spdlog="1.12"
+export libgoogle_cloud_automl_devel="2.24"
+export libtorch="2.1"
+export libgrpc="1.62"
+export libgit2="1.8"
+export readline="8"
+export jpeg="9"
+export libmicrohttpd="1.0"
+export pari="2.15.* *_pthread"
+export libv8="8.9.83"
+export cuda_compiler_version="None"
+export openexr="3.2"
+export nspr="4"
+export libssh2="1"
+export urdfdom="4.0"
+export tiledb="2.23"
+export aws_c_compression="0.2.18"
+export coin_or_utils="2.11"
+export zeromq="4.3.5"
+export libgoogle_cloud_policytroubleshooter_devel="2.24"
+export metis="5.1.0"
+export libraw="0.21"
+export libpq="16"
+export mimalloc="2.1.7"
+export svt_av1="2.1.0"
+export libpcap="1.10"
+export curl="8"
+export lzo="2"
+export idyntree="12"
+export x265="3.5"
+export c_blosc2="2.14"
+export libiconv="1"
+export slepc="3.21"
+export libflint="2.9"
+export libgoogle_cloud_compute_devel="2.24"
+export libvips="8"
+export nlopt="2.7"
+export gstreamer="1.22"
+export libtensorflow_cc="2.15"
+export cutensor="2"
+export aws_c_s3="0.5.9"
+export c_stdlib="sysroot"
+export libode="0.16.2"
+export zlib_ng="2.0"
+export geotiff="1.7.1"
+export libsecret="0.18"
+export libabseil="20240116"
+export hdf5="1.14.3"
+export libmed="4.1"
+export netcdf_fortran="4.6"
+export libptscotch="7.0.4"
+export libcrc32c="1.1"
+export glew="2.1"
+export kealib="1.5"
+export sdl2_image="2"
+export channel_sources="conda-forge,bioconda"
+export harfbuzz="8"
+export nodejs="18"
+export libduckdb_devel="0.9.2"
+export pytorch="2.1"
+export pulseaudio_client="17.0"
+export aws_crt_cpp="0.26.9"
+export pango="1.50"
+export alsa_lib="1.2"
+export bzip2="1"
+export tbb="2021"
+export root_base="6.28.10"
+export libnetcdf="4.9.2"
+export cran_mirror="https://cran.r-project.org"
+export wxwidgets="3.2"
+export orc="2.0.1"
+export singular="4.3.2.p8"
+export libspatialindex="1.9.3"
+export p11_kit="0.24"
+export cuda_compiler="None"
+export log4cxx="1.2.0"
+export cuda_compiler_version_min="11.8"
+export msgpack_cxx="6"
+export libxml2="2"
+export fftw="3"
+export libuuid="2"
+export wcslib="8"
+export VERBOSE_AT="V=1"
+export cudnn="8"
+export mkl="2023"
+export ldas_tools_framecpp="2.9"
+export libgoogle_cloud_aiplatform_devel="2.24"
+export pyqtchart="5.15"
+export qtkeychain="0.14"
+export blas_impl="blis"
+export nss="3"
+export gdk_pixbuf="2"
+export gf2x="1.3"
+export tensorflow="2.15"
+export liblapacke="3.9 *netlib"
+export libgoogle_cloud_spanner_devel="2.24"
+export pcl="1.14.0"
+export krb5="1.21"
+export libsvm="332"
+export libexactreal="4"
+export cgo_compiler="go-cgo"
+export petsc4py="3.21"
+export poppler="24.04"
+export aws_c_event_stream="0.4.2"
+export vtk="9.2.6"
+export libkml="1.3"
+export libssh="0.10"
+export flann="1.9.2"
+export gfal2="2.22"
+export cfitsio="4.3.0"
+export s2n="1.4.15"
+export rdma_core="51"
+export json_c="0.17"
+export zfp="1.0"
+export libgoogle_cloud_devel="2.24"
+export giflib="5.2"
+export soapysdr="0.8"
+export libblas="3.9 *netlib"
+export openjpeg="2"
+export mkl_devel="2023"
+export imath="3.1.11"
+export glib="2"
+export libboost_devel="1.82"
+export target_gobin="${PREFIX}/bin/"
+export libsentencepiece="0.2.0"
+export pugixml="1.14"
+export antic="0.2"
+export libgoogle_cloud_bigtable_devel="2.24"
+export sdl2="2"
+export ipopt="3.14.16"
+export mumps_mpi="5.7.1"
+export qt_main="5.15"
+export c_ares="1"
+export volk="3.1"
+export libgoogle_cloud_pubsub_devel="2.24"
+export aws_c_cal="0.6.14"
+export ffmpeg="6"
+export libunwind="1.6"
+export gmp="6"
+export sdl2_ttf="2"
+export capnproto="1.0.2"
+export isl="0.26"
+export libgoogle_cloud_iam_devel="2.24"
+export libaec="1"
+export tbb_devel="2021"
+export xerces_c="3.2"
+export liblapack="3.9 *netlib"
+export cairo="1"
+export libtiff="4.6"
+export aws_c_io="0.14.8"
+export dav1d="1.2.1"
+export lerc="4"
+export target_goarch="amd64"
+export proj="9.3.1"
+export arb="2.23"
+export aws_c_mqtt="0.10.4"
+export libgoogle_cloud_speech_devel="2.24"
+export expat="2"
+export bullet_cpp="3.25"
+export srm_ifce="1.24.6"
+export libgoogle_cloud_storage_devel="2.24"
+export libavif="1"
+export postgresql="16"
+export glpk="5.0"
+export graphviz="9"
+export lmdb="0.9.29"
+export flatbuffers="24.3.25"
+export libxsmm="1"
+export freetype="2"
+export console_bridge="1.0"
+export libgoogle_cloud="2.24"
+export aom="3.8"
+export rust_compiler="rust"
+export libgoogle_cloud_all_devel="2.24"
+export libdeflate="1.20"
+export nccl="2"
+export libgoogle_cloud_discoveryengine_devel="2.24"
+export attr="2.5"
+export gsoap="2.8.123"
+export starlink_ast="9.2.7"
+export fortran_compiler="gfortran"
+export r_base="4.3.*"
+export libwebp="1"
+export libsndfile="1.2"
+export poco="1.13.3"
+export libosqp="0.6.3"
+export arrow_cpp="15"
+export libarrow="15"
+export libarrow_all="15"
+export python_impl="cpython"
+export c_stdlib_version="2.17"
+export cdt_name="cos6"
+export c_compiler_version="12"
+export cxx_compiler_version="12"
+export fortran_compiler_version="12"
+export CONDA_BUILD_STATE="BUILD"
+export PIP_NO_BUILD_ISOLATION="False"
+export PIP_NO_DEPENDENCIES="True"
+export PIP_IGNORE_INSTALLED="True"
+export PIP_CACHE_DIR="/opt/conda/conda-bld/jbrowse2_1726856947541/pip_cache"
+export PIP_NO_INDEX="True"
+eval "$('/opt/conda/bin/python' -m conda shell.bash hook)"
+conda activate "/home/ross/miniconda3/envs/mulled-v1-ead19212d339c2197ed3232dcd8366627d23ccb1cf4fb8ae3186545effdca881"
+conda activate --stack "/opt/conda/conda-bld/jbrowse2_1726856947541/_build_env"