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| author | Toyohisa Kameyama <kameyama@riken.jp> | 2019-10-04 12:19:58 +0900 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2019-10-03 22:19:58 -0500 |
| commit | b89fa3e01a67308ec41398e2a888526b014664cb (patch) | |
| tree | 0b5d23f624af77f055bb4a81fe7efa7986f689bf | |
| parent | 4046e10b951cf6c5f420fa125d6bea23103b60f8 (diff) | |
| download | spack-b89fa3e01a67308ec41398e2a888526b014664cb.tar.gz spack-b89fa3e01a67308ec41398e2a888526b014664cb.tar.bz2 spack-b89fa3e01a67308ec41398e2a888526b014664cb.tar.xz spack-b89fa3e01a67308ec41398e2a888526b014664cb.zip | |
fastqvalidator: add zlib dependency and Removes erroneous deletes in Chromosome (#13030)
| -rw-r--r-- | var/spack/repos/builtin/packages/fastqvalidator/chromosome.patch | 26 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/fastqvalidator/package.py | 3 |
2 files changed, 29 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/fastqvalidator/chromosome.patch b/var/spack/repos/builtin/packages/fastqvalidator/chromosome.patch new file mode 100644 index 0000000000..579444868e --- /dev/null +++ b/var/spack/repos/builtin/packages/fastqvalidator/chromosome.patch @@ -0,0 +1,26 @@ +commit 3a10afe08c209dbacc3eca7794a5a8c0a42ee566 +Author: jonathonl <jonathonl@users.noreply.github.com> +Date: Thu Sep 20 11:57:06 2018 -0400 + + Removes erroneous deletes in Chromosome constructor. + +diff --git a/general/Chromosome.cpp b/general/Chromosome.cpp +index ac2ff5c..2d773e8 100644 +--- a/general/Chromosome.cpp ++++ b/general/Chromosome.cpp +@@ -27,7 +27,6 @@ Chromosome::Chromosome(GenomeSequence* gs, const char* chromosomeName) + Chromosome::Chromosome(const char* genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace) + { + std::string s(genomseSequenceFileName); +- if (this->gs) delete gs; + gs = new GenomeSequence; + assert(gs); + gs->setReferenceName(s); +@@ -39,7 +38,6 @@ Chromosome::Chromosome(const char* genomseSequenceFileName, unsigned int chromos + + Chromosome::Chromosome(const std::string& genomseSequenceFileName, unsigned int chromosomeIndex, bool isColorSpace) + { +- if (this->gs) delete gs; + gs = new GenomeSequence; + assert(gs); + gs->setReferenceName(genomseSequenceFileName); diff --git a/var/spack/repos/builtin/packages/fastqvalidator/package.py b/var/spack/repos/builtin/packages/fastqvalidator/package.py index 4395892e17..9397eec2a0 100644 --- a/var/spack/repos/builtin/packages/fastqvalidator/package.py +++ b/var/spack/repos/builtin/packages/fastqvalidator/package.py @@ -20,6 +20,9 @@ class Fastqvalidator(MakefilePackage): commit='9db9c23e176a6ce6f421a3c21ccadedca892ac0c' ) + depends_on('zlib', type='link') + patch('chromosome.patch', when='@2017-01-10', working_dir='libStatGen') + @property def build_targets(self): return ['LIB_PATH_GENERAL={0}'.format( |