Update masurca: adding missing dependencies

[LiaOb21]

I'm updating the recipe for masurca as building its nf-core module we realised some dependencies are missing, causing the biocontainer associated with this recipe to not be functional: nf-core/modules#11049

added dependencies:
- cmake
- xz
- ncurses
- openssl
- gdbm
- python
- file
- gzip
- coreutils

Also, I added:

  skip-lints:
    - compiler_needs_stdlib_c  # until https://github.com/bioconda/bioconda-utils/issues/1095 is resolved

as seen in other recipes, as bioconda/bioconda-utils#1095 (comment) still appears to be an issue

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[LiaOb21]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	masurca-4.1.4-ha5bb246_1.conda	linux-64.zip	GitHub Actions	show You may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>

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Docker image(s) built:

Package	Tag	CI	Install with docker
masurca	4.1.4--ha5bb246_1	GitHub Actions	show Images are in the linux-64 zip file above.gzip -dc images/masurca---4.1.4--ha5bb246_1.tar.gz | docker load

[LiaOb21]

Both conda package and docker locally tested and producing expected outputs.

[LiaOb21]

@BiocondaBot please add label

[LiaOb21]

Found problem when testing docker container with jump reads:

./assemble.sh: line 146: /usr/local/bin/filter_alt.pl: cannot execute: required file not found
./assemble.sh: line 148: /usr/local/bin/filter_alt.pl: cannot execute: required file not found

Attempting to resolve by adding find "${PREFIX}/bin" -name "*.pl" -exec sed -i '1s|^#!.*perl.*|#!/usr/bin/env perl|' {} + to build.sh to fix hardcoded perl shebangs to use env

[LiaOb21]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	masurca-4.1.4-ha5bb246_1.conda	linux-64.zip	GitHub Actions	show You may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>

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Docker image(s) built:

Package	Tag	CI	Install with docker
masurca	4.1.4--ha5bb246_1	GitHub Actions	show Images are in the linux-64 zip file above.gzip -dc images/masurca---4.1.4--ha5bb246_1.tar.gz | docker load

[LiaOb21]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	masurca-4.1.4-ha5bb246_1.conda	linux-64.zip	GitHub Actions	show You may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>

---

Docker image(s) built:

Package	Tag	CI	Install with docker
masurca	4.1.4--ha5bb246_1	GitHub Actions	show Images are in the linux-64 zip file above.gzip -dc images/masurca---4.1.4--ha5bb246_1.tar.gz | docker load

[LiaOb21]

Tested locally with both conda and docker with the following input combinations:

• paired end
• single end
• paired end + jump reads
• paired end + ONT
• paired end + PacBio
• pared end + ONT + PacBio

All working

[LiaOb21]

@Mergifyio queue

[mergify]

queue

☑️ Command disallowed due to command restrictions in the Mergify configuration.

Details

• sender-permission >= write