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jts / smrest

Tumour-only somatic mutation calling using long reads
MIT License
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Needs Bioperl to compile properly #1

Open adbeggs opened 7 months ago

adbeggs commented 7 months ago

Hi Jared

Thanks very much for this, looks great. Struggled to compile it with our default HPC setup, seems to need Bioperl so when I added this into the module loading it worked fine - just thought you might want to flag that up as a dependency?

Thanks

Andrew

error: failed to run custom build command for `openssl-sys v0.9.101`

Caused by:
  process didn't exit successfully: `/rds/projects/b/beggsa-clinicalnanopore/software/smrest/target/release/build/openssl-sys-2faa01a08fa781ec/build-script-main` (exit status: 101)
  --- stdout
  cargo:rerun-if-env-changed=X86_64_UNKNOWN_LINUX_GNU_OPENSSL_NO_VENDOR
  X86_64_UNKNOWN_LINUX_GNU_OPENSSL_NO_VENDOR unset
  cargo:rerun-if-env-changed=OPENSSL_NO_VENDOR
  OPENSSL_NO_VENDOR unset
  cargo:rerun-if-env-changed=CC_x86_64-unknown-linux-gnu
  CC_x86_64-unknown-linux-gnu = None
  cargo:rerun-if-env-changed=CC_x86_64_unknown_linux_gnu
  CC_x86_64_unknown_linux_gnu = None
  cargo:rerun-if-env-changed=HOST_CC
  HOST_CC = None
  cargo:rerun-if-env-changed=CC
  CC = None
  cargo:rerun-if-env-changed=CC_ENABLE_DEBUG_OUTPUT
  cargo:rerun-if-env-changed=CRATE_CC_NO_DEFAULTS
  CRATE_CC_NO_DEFAULTS = None
  DEBUG = Some("false")
  CARGO_CFG_TARGET_FEATURE = Some("fxsr,sse,sse2")
  cargo:rerun-if-env-changed=CFLAGS_x86_64-unknown-linux-gnu
  CFLAGS_x86_64-unknown-linux-gnu = None
  cargo:rerun-if-env-changed=CFLAGS_x86_64_unknown_linux_gnu
  CFLAGS_x86_64_unknown_linux_gnu = None
  cargo:rerun-if-env-changed=HOST_CFLAGS
  HOST_CFLAGS = None
  cargo:rerun-if-env-changed=CFLAGS
  CFLAGS = None
  cargo:rerun-if-env-changed=AR_x86_64-unknown-linux-gnu
  AR_x86_64-unknown-linux-gnu = None
  cargo:rerun-if-env-changed=AR_x86_64_unknown_linux_gnu
  AR_x86_64_unknown_linux_gnu = None
  cargo:rerun-if-env-changed=HOST_AR
  HOST_AR = None
  cargo:rerun-if-env-changed=AR
  AR = None
  cargo:rerun-if-env-changed=ARFLAGS_x86_64-unknown-linux-gnu
  ARFLAGS_x86_64-unknown-linux-gnu = None
  cargo:rerun-if-env-changed=ARFLAGS_x86_64_unknown_linux_gnu
  ARFLAGS_x86_64_unknown_linux_gnu = None
  cargo:rerun-if-env-changed=HOST_ARFLAGS
  HOST_ARFLAGS = None
  cargo:rerun-if-env-changed=ARFLAGS
  ARFLAGS = None
  cargo:rerun-if-env-changed=RANLIB_x86_64-unknown-linux-gnu
  RANLIB_x86_64-unknown-linux-gnu = None
  cargo:rerun-if-env-changed=RANLIB_x86_64_unknown_linux_gnu
  RANLIB_x86_64_unknown_linux_gnu = None
  cargo:rerun-if-env-changed=HOST_RANLIB
  HOST_RANLIB = None
  cargo:rerun-if-env-changed=RANLIB
  RANLIB = None
  cargo:rerun-if-env-changed=RANLIBFLAGS_x86_64-unknown-linux-gnu
  RANLIBFLAGS_x86_64-unknown-linux-gnu = None
  cargo:rerun-if-env-changed=RANLIBFLAGS_x86_64_unknown_linux_gnu
  RANLIBFLAGS_x86_64_unknown_linux_gnu = None
  cargo:rerun-if-env-changed=HOST_RANLIBFLAGS
  HOST_RANLIBFLAGS = None
  cargo:rerun-if-env-changed=RANLIBFLAGS
  RANLIBFLAGS = None
  running cd "/rds/projects/b/beggsa-clinicalnanopore/software/smrest/target/release/build/openssl-sys-2e3c4926f6f1a567/out/openssl-build/build/src" && AR="ar" CC="cc" RANLIB="ranlib" "perl" "./Configure" "--prefix=/rds/projects/b/beggsa-clinicalnanopore/software/smrest/target/release/build/openssl-sys-2e3c4926f6f1a567/out/openssl-build/install" "--openssldir=/usr/local/ssl" "no-dso" "no-shared" "no-ssl3" "no-tests" "no-comp" "no-zlib" "no-zlib-dynamic" "--libdir=lib" "no-md2" "no-rc5" "no-weak-ssl-ciphers" "no-camellia" "no-idea" "no-seed" "linux-x86_64" "-O2" "-ffunction-sections" "-fdata-sections" "-fPIC" "-m64"

  --- stderr
  Can't locate IPC/Cmd.pm in @INC (you may need to install the IPC::Cmd module) (@INC contains: /rds/projects/b/beggsa-clinicalnanopore/software/smrest/target/release/build/openssl-sys-2e3c4926f6f1a567/out/openssl-build/build/src/util/perl /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 /rds/projects/b/beggsa-clinicalnanopore/software/smrest/target/release/build/openssl-sys-2e3c4926f6f1a567/out/openssl-build/build/src/external/perl/Text-Template-1.56/lib) at /rds/projects/b/beggsa-clinicalnanopore/software/smrest/target/release/build/openssl-sys-2e3c4926f6f1a567/out/openssl-build/build/src/util/perl/OpenSSL/config.pm line 19.
  BEGIN failed--compilation aborted at /rds/projects/b/beggsa-clinicalnanopore/software/smrest/target/release/build/openssl-sys-2e3c4926f6f1a567/out/openssl-build/build/src/util/perl/OpenSSL/config.pm line 19.
  Compilation failed in require at ./Configure line 23.
  BEGIN failed--compilation aborted at ./Configure line 23.
  thread 'main' panicked at /rds/homes/b/beggsa/.cargo/registry/src/index.crates.io-6f17d22bba15001f/openssl-src-300.2.3+3.2.1/src/lib.rs:611:9:

  Error configuring OpenSSL build:
      Command: cd "/rds/projects/b/beggsa-clinicalnanopore/software/smrest/target/release/build/openssl-sys-2e3c4926f6f1a567/out/openssl-build/build/src" && AR="ar" CC="cc" RANLIB="ranlib" "perl" "./Configure" "--prefix=/rds/projects/b/beggsa-clinicalnanopore/software/smrest/target/release/build/openssl-sys-2e3c4926f6f1a567/out/openssl-build/install" "--openssldir=/usr/local/ssl" "no-dso" "no-shared" "no-ssl3" "no-tests" "no-comp" "no-zlib" "no-zlib-dynamic" "--libdir=lib" "no-md2" "no-rc5" "no-weak-ssl-ciphers" "no-camellia" "no-idea" "no-seed" "linux-x86_64" "-O2" "-ffunction-sections" "-fdata-sections" "-fPIC" "-m64"
      Exit status: exit status: 2
jts commented 7 months ago

Thanks for the early feedback @adbeggs. I don't think Bioperl specifically needs to be installed but openssl does seem to need some perl libraries. I'll look into this more and probably provide pre-compiled binaries on the releases page to make the use of the program easier.