Comments (2)
I'm having a similar problem, although for me it's Libiconv that says it wasn't installed correctly. This is the complete output when I try to run Baysor:
~/Baysor/bin$ ./baysor run --help
fatal: error thrown and no exception handler available.
InitError(mod=:Libiconv_jll, error=ErrorException("Artifact "Libiconv" was not installed correctly. Try `using Pkg; Pkg.instantiate()` to re-install all missing resources."))
error at ./error.jl:33
_artifact_str at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Artifacts/src/Artifacts.jl:551
jfptr__artifact_str_52381 at /home/jckern/Baysor/bin/julia-1.6.0/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2237 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2419
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1703 [inlined]
jl_f__call_latest at /buildworker/worker/package_linux64/build/src/builtins.c:714
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2237 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2419
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1703 [inlined]
do_apply at /buildworker/worker/package_linux64/build/src/builtins.c:670
#invokelatest#2 at ./essentials.jl:708
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2237 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2419
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1703 [inlined]
do_apply at /buildworker/worker/package_linux64/build/src/builtins.c:670
invokelatest at ./essentials.jl:706
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2237 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2419
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1703 [inlined]
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:115
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:204
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:155 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:561
jl_fptr_interpret_call at /buildworker/worker/package_linux64/build/src/interpreter.c:649
macro expansion at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Artifacts/src/Artifacts.jl:680 [inlined]
find_artifact_dir at /home/jckern/Baysor/bin/.julia/packages/JLLWrappers/WnWcZ/src/wrapper_generators.jl:15
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2237 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2419
__init__ at /home/jckern/Baysor/bin/.julia/packages/Libiconv_jll/bLsPg/src/wrappers/x86_64-linux-gnu.jl:8
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2237 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2419
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1703 [inlined]
jl_module_run_initializer at /buildworker/worker/package_linux64/build/src/toplevel.c:72
_julia_init at /buildworker/worker/package_linux64/build/src/init.c:794
repl_entrypoint at /buildworker/worker/package_linux64/build/src/jlapi.c:696
main at /buildworker/worker/package_linux64/build/cli/loader_exe.c:51
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_start at /home/jckern/Baysor/bin/julia-1.6.0//bin/julia (unknown line)
from baysor.
I was able to install version 0.4.3 as a Julia package by running
using Pkg
Pkg.add([PackageSpec(name="UMAP", rev="master"), PackageSpec(url="https://github.com/kharchenkolab/Baysor.git")])
import Baysor
in Julia and
echo "#! /usr/bin/env julia\nimport Baysor: run_cli\nrun_cli()" >> baysor && chmod +x baysor
in the terminal. But, I had to change the path to Julia and fix the newline issue.
from baysor.
Related Issues (20)
- Version Flag states "nothing" HOT 2
- Error: Not enough prior cells pass the min_mols_per_cell=10 threshold HOT 4
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- clustering transcripts without segmentation HOT 3
- Baysor segmentation HOT 5
- --save-polygons=geojson only creates .json file not .geojson HOT 10
- Prior Segmentation TIFF Image cannot be loaded and returns an error HOT 2
- Surprised at the poor result despite with accurate Prior Segmentation HOT 2
- BUG: segmentation_polygon.json produce polygon with only 2 points HOT 1
- Issue when running Baysor with prior segmentation HOT 4
- Error: System image file failed consistency check: maybe opened the wrong version? HOT 3
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from baysor.