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* Merge pull request #295208 from r-ryantm/auto-update/igvPol Dellaiera2024-03-12
|\ | | | | igv: 2.17.2 -> 2.17.3
| * igv: 2.17.2 -> 2.17.3R. Ryantm2024-03-12
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* | seqkit: 2.7.0 -> 2.8.0R. Ryantm2024-03-12
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* Merge pull request #285423 from r-ryantm/auto-update/diamondWeijia Wang2024-03-07
|\ | | | | diamond: 2.1.8 -> 2.1.9
| * diamond: 2.1.8 -> 2.1.9R. Ryantm2024-02-01
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* | Merge pull request #287668 from r-ryantm/auto-update/igvWeijia Wang2024-03-07
|\ \ | | | | | | igv: 2.17.1 -> 2.17.2
| * | igv: 2.17.1 -> 2.17.2R. Ryantm2024-02-10
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* | | Merge pull request #289911 from r-ryantm/auto-update/lastJustin Bedő2024-03-01
|\ \ \ | | | | | | | | last: 1541 -> 1542
| * | | last: 1541 -> 1542R. Ryantm2024-02-19
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* | | | sortmerna: fix `gcc-13` buildSergei Trofimovich2024-02-25
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Without the change the build on `master` fails as https://hydra.nixos.org/build/249070958: In file included from /build/source/src/sortmerna/kseq_load.cpp:38: /build/source/include/kseq_load.hpp:61:12: error: 'uint64_t' has not been declared 61 | uint64_t number_total_read, | ^~~~~~~~
* | | | octopus-caller: fix `gcc-13` build failure (drop `-Werror`)Sergei Trofimovich2024-02-20
|/ / / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Without the change the build on `master` fails as https://hydra.nixos.org/build/249090788: /build/source/src/config/option_collation.cpp: In function 'auto octopus::options::make_variant_generator_builder(const OptionMap&, boost::optional<const octopus::ReadSetProfile&>)': /build/source/src/config/option_collation.cpp:1298: error: redundant move in initialization [-Werror=redundant-move] 1298 | throw ConflictingSourceVariantFile {std::move(source_path), *output_path}; | Blanket `-Werror` frequently causes build failures unless upstream is quick at addressing build failures.
* | | last: 1540 -> 1541R. Ryantm2024-02-14
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* | | Merge pull request #287721 from trofi/megahit-gcc-13-fixkirillrdy2024-02-14
|\ \ \ | | | | | | | | megahit: fix `gcc-13` build failure
| * | | megahit: fir `gcc-13` build failureSergei Trofimovich2024-02-10
| |/ / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Without the change build fails on `master` against `gcc-13` as https://hydra.nixos.org/build/247673319: In file included from /build/source/src/main_local_assemble.cpp:27: /build/source/src/localasm/local_assemble.h:31:3: error: 'uint32_t' does not name a type 31 | uint32_t kmin{11}; | ^~~~~~~~ /build/source/src/localasm/local_assemble.h:1:1: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'? +++ |+#include <cstdint>
* | | Merge pull request #287985 from trofi/svaba-gcc-13-fixkirillrdy2024-02-14
|\ \ \ | | | | | | | | svaba: fix `gcc-13` build failure
| * | | svaba: fix `gcc-13` build failureSergei Trofimovich2024-02-11
| |/ / | | | | | | | | | | | | | | | | | | | | | | | | | | | Without the change build fails on `master` as https://hydra.nixos.org/build/249164637: In file included from Histogram.cpp:1: Histogram.h:104:61: error: 'uint32_t' does not name a type 104 | Histogram(const int32_t& start, const int32_t& end, const uint32_t& width); | ^~~~~~~~
* | | Merge pull request #286906 from ashgillman/masterNick Cao2024-02-11
|\ \ \ | |/ / |/| | dcm2niix: 1.0.20211006 -> 1.0.20230411
| * | dcm2niix: 1.0.20211006 -> 1.0.20230411Ashley Gillman2024-02-07
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* | | hh-suite: fix build on GCC 13Manuel Frischknecht2024-02-08
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The build of `hh-suite` stopped working with GCC 13 because GCC stopped transitively including a couple of headers like `cstdint` in various scenarios. There already is an upstream PR proposed that fixes this issue [1] but hasn't been merged yet. This change pulls in this correction using `fetchpatch`, fixing the build for now. [1]: https://github.com/soedinglab/hh-suite/pull/357
* | | last: 1519 -> 1540R. Ryantm2024-02-06
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* | Merge pull request #285426 from r-ryantm/auto-update/seqkitRobert Scott2024-02-04
|\ \ | | | | | | seqkit: 2.6.1 -> 2.7.0
| * | seqkit: 2.6.1 -> 2.7.0R. Ryantm2024-02-01
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* | Merge pull request #281847 from r-ryantm/auto-update/eggnog-mapperWeijia Wang2024-02-04
|\ \ | | | | | | eggnog-mapper: 2.1.10 -> 2.1.12
| * | eggnog-mapper: 2.1.10 -> 2.1.12R. Ryantm2024-01-18
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* | | Merge pull request #281665 from r-ryantm/auto-update/bowtie2Weijia Wang2024-02-04
|\ \ \ | | | | | | | | bowtie2: 2.5.2 -> 2.5.3
| * | | bowtie2: 2.5.2 -> 2.5.3R. Ryantm2024-01-18
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* | | igv: use jdk17 instead of jdk11 (#285521)Rolf Schröder2024-02-01
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* | | Merge pull request #222817 from SuperSandro2000/python-sitePackagesPeder Bergebakken Sundt2024-01-31
|\ \ \ | | | | | | | | treewide: replace `lib/${python.libPrefix}/site-packages` with its sh…
| * | | treewide: replace `lib/${python.libPrefix}/site-packages` with its shorthand ↵Sandro Jäckel2024-01-30
| | | | | | | | | | | | | | | | | | | | | | | | `${python.sitePackages}` which should be always preferred
* | | | Merge pull request #284607 from dotlambda/deeptools-fixSandro2024-01-30
|\ \ \ \ | |_|_|/ |/| | | deeptools: fix build
| * | | deeptools: fix buildRobert Schütz2024-01-28
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* | | | samtools: 1.19 -> 1.19.2R. Ryantm2024-01-28
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* | | Merge pull request #283816 from trofi/whisper-gcc-13-fixMaximilian Bosch2024-01-26
|\ \ \ | | | | | | | | whisper: fix `gcc-13` build failure
| * | | whisper: enable parallel buildingSergei Trofimovich2024-01-25
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| * | | whisper: fix `gcc-13` build failureSergei Trofimovich2024-01-25
| |/ / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Without the change build fails on `master` against `gcc-13` as https://hydra.nixos.org/build/246505636: mapper/../common/defs.h:53:9: error: 'uint32_t' does not name a type 53 | typedef uint32_t ref_pos_t; | ^~~~~~~~ mapper/../common/defs.h:35:1: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'? 34 | #include <string> +++ |+#include <cstdint>
* / / ants: 2.5.0 -> 2.5.1R. Ryantm2024-01-26
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* | Merge pull request #283425 from r-ryantm/auto-update/stacksNick Cao2024-01-24
|\ \ | | | | | | stacks: 2.65 -> 2.66
| * | stacks: 2.65 -> 2.66R. Ryantm2024-01-24
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* | | igv: 2.17.0 -> 2.17.1R. Ryantm2024-01-24
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* | Merge pull request #282666 from wegank/ebtks-refactorWeijia Wang2024-01-23
|\ \ | | | | | | ebtks: fix build on darwin, refactor
| * | inormalize: fix build on darwinWeijia Wang2024-01-21
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| * | n3: fix build on darwinWeijia Wang2024-01-21
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| * | ebtks: migrate to by-name, rename from EBTKSWeijia Wang2024-01-21
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* / SPAdes: fix buildsuperherointj2024-01-20
|/ | | | | | Fixes #282372 Co-authored-by: @wegank
* Merge pull request #279509 from r-ryantm/auto-update/igvWeijia Wang2024-01-13
|\ | | | | igv: 2.16.2 -> 2.17.0
| * igv: 2.16.2 -> 2.17.0R. Ryantm2024-01-08
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* | Merge pull request #278776 from TomaSajt/trimmomaticWeijia Wang2024-01-11
|\ \ | |/ |/| trimmomatic: make deterministic and clean up
| * trimmomatic: make deterministic and clean upTomaSajt2024-01-04
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* | Merge pull request #276101 from r-ryantm/auto-update/dellyWeijia Wang2024-01-03
|\ \ | |/ |/| delly: 1.1.8 -> 1.2.6
| * delly: 1.1.8 -> 1.2.6R. Ryantm2023-12-22
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