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snakemake -jall not working on macOS #17

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lorenzomancini1 opened this issue Nov 21, 2023 · 0 comments
Open

snakemake -jall not working on macOS #17

lorenzomancini1 opened this issue Nov 21, 2023 · 0 comments

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@lorenzomancini1
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Hello, when I try to run the snakemake -jall command, I get this error env: illegal option -- C.

I tried to solve it by modifying the Snakefile rules where the env -C /desired/path/ ... command is required by replacing it with (cd /desired/path/ && ...). In this way the configure rules are working but I get an error from the build rules:

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job stats:
job                count
---------------  -------
all                    1
build                  2
build_veins            2
build_veins_vlc        2
total                  7

Select jobs to execute...

[Mon Nov 20 11:16:38 2023]
rule build_veins:
    input: lib/veins/src/Makefile
    output: lib/veins/src/libveins.so
    jobid: 9
    reason: Missing output files: lib/veins/src/libveins.so
    wildcards: dbg=
    threads: 4
    resources: tmpdir=/var/folders/qx/8mj8c3js6zdfblrg8s_5rqtr0000gn/T

[Mon Nov 20 11:16:38 2023]
Error in rule build_veins:
    jobid: 9
    input: lib/veins/src/Makefile
    output: lib/veins/src/libveins.so
    shell:
        make -j4 -C lib/veins/src MODE=release
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-11-20T111637.880905.snakemake.log

If I try to run the rule of build_veins by running make -j4 -C lib/veins/src MODE=release I get:

make: *** No rule to make target ../out/clang-release/src/veins/base/connectionManager/BaseConnectionManager.o', needed by ../out/clang-release/src/libveins.dylib'.  Stop.

Can anyone help me?

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