Update mosdepth recipe

[ramprasadn]

This update relates to the issue descibed at brentp/mosdepth#232

---

Please read the guidelines for Bioconda recipes before opening a pull request (PR).

General instructions

• If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
• New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
• PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
• Please post questions on Gitter or ping @bioconda/core in a comment.

Instructions for avoiding API, ABI, and CLI breakage issues

Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify run_exports (see here for the rationale and comprehensive explanation).
Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case	run_exports statement
semantic versioning	{{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x)	{{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions	{{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions	{{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning	{{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

Bot commands for PR management

Please use the following BiocondaBot commands:

Everyone has access to the following BiocondaBot commands, which can be given in a comment:

@BiocondaBot please update	Merge the master branch into a PR.
@BiocondaBot please add label	Add the please review & merge label.
@BiocondaBot please fetch artifacts	Post links to CI-built packages/containers. You can use this to test packages locally.

Note that the @BiocondaBot please merge command is now depreciated. Please just squash and merge instead.

Also, the bot watches for comments from non-members that include @bioconda/<team> and will automatically re-post them to notify the addressed <team>.

[ramprasadn]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	mosdepth-0.3.8-hd299d5a_1.tar.bz2	LinuxArtifacts.zip	Azure	show You may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
osx-64	mosdepth-0.3.8-h212548b_1.tar.bz2	OSXArtifacts.zip	Azure	show You may also use conda to install after downloading and extracting the zip file. From the OSXArtifacts directory: conda install -c ./packages <package name>

---

Docker image(s) built:

Package	Tag	CI	Install with docker
mosdepth	0.3.8--hd299d5a_1	Azure	show Images for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/mosdepth:0.3.8--hd299d5a_1.tar.gz | docker load

[ramprasadn]

Hey @brentp, do you happen to know why the compilation is not successful on osx? It seems that d4 is installed correctly, but the compilation with nim is failing.

[ramprasadn]

Tried to compile the package on my laptop, following the steps defined in the build.sh. I got this

❯ nimble build -y --verbose -d:d4 -d:release
  Verifying dependencies for mosdepth@0.3.8
    Reading official package list
   Checking for hts@>= 0.3.22
      Info: Dependency on hts@>= 0.3.22 already satisfied
  Verifying dependencies for hts@0.3.25
    Reading official package list
   Checking for docopt@0.7.0
      Info: Dependency on docopt@0.7.0 already satisfied
  Verifying dependencies for docopt@0.7.0
    Reading official package list
   Checking for regex@>= 0.11.1
      Info: Dependency on regex@>= 0.11.1 already satisfied
  Verifying dependencies for regex@0.25.0
    Reading official package list
   Checking for unicodedb@>= 0.7.2
      Info: Dependency on unicodedb@>= 0.7.2 already satisfied
  Verifying dependencies for unicodedb@0.12.0
    Reading official package list
   Checking for https://github.com/brentp/d4-nim@>= 0.0.3
      Info: Dependency on https://github.com/brentp/d4-nim@>= 0.0.3 already satisfied
  Verifying dependencies for d4@0.0.3
   Building mosdepth/mosdepth using c backend
  Executing /Users/ramp/Documents/nim-1.6.21/bin/nim c --colors:on --noNimblePath -d:d4 -d:release -d:NimblePkgVersion=0.3.8 --path:/Users/ramp/.nimble/pkgs/hts-0.3.25 --path:/Users/ramp/.nimble/pkgs/docopt-0.7.0 --path:/Users/ramp/.nimble/pkgs/regex-0.25.0 --path:/Users/ramp/.nimble/pkgs/unicodedb-0.12.0 --path:/Users/ramp/.nimble/pkgs/d4-0.0.3 -o:/Users/ramp/Documents/mosdepth-0.3.8/mosdepth /Users/ramp/Documents/mosdepth-0.3.8/mosdepth.nim
Hint: used config file '/Users/ramp/Documents/nim-1.6.21/config/nim.cfg' [Conf]
Hint: used config file '/Users/ramp/Documents/nim-1.6.21/config/config.nims' [Conf]
Hint: used config file '/Users/ramp/Documents/mosdepth-0.3.8/nim.cfg' [Conf]
.............................................................................................................................................
/Users/ramp/Documents/mosdepth-0.3.8/mosdepth.nim(265, 18) template/generic instantiation of `tag` from here
/Users/ramp/.nimble/pkgs/hts-0.3.25/hts/bam/auxtags.nim(63, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode]
/Users/ramp/Documents/mosdepth-0.3.8/mosdepth.nim(265, 18) template/generic instantiation of `tag` from here
/Users/ramp/.nimble/pkgs/hts-0.3.25/hts/bam/auxtags.nim(66, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode]
/Users/ramp/Documents/mosdepth-0.3.8/mosdepth.nim(265, 18) template/generic instantiation of `tag` from here
/Users/ramp/.nimble/pkgs/hts-0.3.25/hts/bam/auxtags.nim(74, 7) Warning: unreachable code after 'return' statement or '{.noReturn.}' proc [UnreachableCode]
/Users/ramp/Documents/mosdepth-0.3.8/mosdepth.nim(609, 15) Warning: open; wopen_bgzi is deprecated [Deprecated]
/Users/ramp/Documents/mosdepth-0.3.8/mosdepth.nim(612, 17) Warning: open; wopen_bgzi is deprecated [Deprecated]
/Users/ramp/Documents/mosdepth-0.3.8/mosdepth.nim(615, 19) Warning: open; wopen_bgzi is deprecated [Deprecated]
/Users/ramp/Documents/mosdepth-0.3.8/mosdepth.nim(628, 15) Warning: open; wopen_bgzi is deprecated [Deprecated]
/Users/ramp/Documents/mosdepth-0.3.8/mosdepth.nim(889, 13) Warning: implicit conversion to 'cstring' from a non-const location: $args["<BAM-or-CRAM>"]; this will become a compile time error in the future [CStringConv]
/Users/ramp/Documents/mosdepth-0.3.8/mosdepth.nim(11, 8) Warning: imported and not used: 'times' [UnusedImport]
CC: ../nim-1.6.21/lib/system.nim
CC: ../nim-1.6.21/lib/pure/unicode.nim
CC: ../nim-1.6.21/lib/pure/math.nim
CC: ../nim-1.6.21/lib/pure/algorithm.nim
CC: ../nim-1.6.21/lib/pure/strutils.nim
CC: ../nim-1.6.21/lib/pure/strformat.nim
CC: ../../.nimble/pkgs/hts-0.3.25/hts/bam.nim
CC: ../nim-1.6.21/lib/pure/collections/tables.nim
CC: depthstat.nim
CC: ../../.nimble/pkgs/d4-0.0.3/d4.nim
CC: mosdepth.nim
/Users/ramp/.cache/nim/mosdepth_r/@m..@s..@s.nimble@spkgs@sd4-0.0.3@sd4.nim.c:8:10: fatal error: 'd4.h' file not found
#include <d4.h>
         ^~~~~~
1 error generated.
Error: execution of an external compiler program 'clang -c  -w -ferror-limit=3 -O3   -I/Users/ramp/Documents/nim-1.6.21/lib -I/Users/ramp/Documents/mosdepth-0.3.8 -o /Users/ramp/.cache/nim/mosdepth_r/@m..@s..@s.nimble@spkgs@sd4-0.0.3@sd4.nim.c.o /Users/ramp/.cache/nim/mosdepth_r/@m..@s..@s.nimble@spkgs@sd4-0.0.3@sd4.nim.c' failed with exit code: 1


     Error: Build failed for package: mosdepth
        ... Execution failed with exit code 256
        ... Command: /Users/ramp/Documents/nim-1.6.21/bin/nim c --colors:on --noNimblePath -d:d4 -d:release -d:NimblePkgVersion=0.3.8 --path:/Users/ramp/.nimble/pkgs/hts-0.3.25 --path:/Users/ramp/.nimble/pkgs/docopt-0.7.0 --path:/Users/ramp/.nimble/pkgs/regex-0.25.0 --path:/Users/ramp/.nimble/pkgs/unicodedb-0.12.0 --path:/Users/ramp/.nimble/pkgs/d4-0.0.3 -o:/Users/ramp/Documents/mosdepth-0.3.8/mosdepth /Users/ramp/Documents/mosdepth-0.3.8/mosdepth.nim

[martin-g]

The build passes now but it fails at runtime with:

+ mosdepth -h�[0m
2024-06-07T12:58:45.6161050Z 12:58:36 �[32mBIOCONDA INFO�[0m (ERR) dyld[11315]: Library not loaded: '/usr/local/miniconda/envs/bioconda/conda-bld/d4binding_1646531208915/work/target/release/deps/libd4binding.dylib'�[0m
2024-06-07T12:58:45.6164930Z 12:58:36 �[32mBIOCONDA INFO�[0m (ERR)   Referenced from: '/opt/mambaforge/envs/bioconda/conda-bld/mosdepth_1717764904907/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/bin/mosdepth'�[0m
2024-06-07T12:58:45.6170790Z 12:58:36 �[32mBIOCONDA INFO�[0m (ERR)   Reason: tried: '/usr/local/miniconda/envs/bioconda/conda-bld/d4binding_1646531208915/work/target/release/deps/libd4binding.dylib' (no such file), '/usr/local/lib/libd4binding.dylib' (no such file), '/usr/lib/libd4binding.dylib' (no such file)�[0m

[martin-g]

The build passes now but it fails at runtime with:

+ mosdepth -h�[0m
2024-06-07T12:58:45.6161050Z 12:58:36 �[32mBIOCONDA INFO�[0m (ERR) dyld[11315]: Library not loaded: '/usr/local/miniconda/envs/bioconda/conda-bld/d4binding_1646531208915/work/target/release/deps/libd4binding.dylib'�[0m
2024-06-07T12:58:45.6164930Z 12:58:36 �[32mBIOCONDA INFO�[0m (ERR)   Referenced from: '/opt/mambaforge/envs/bioconda/conda-bld/mosdepth_1717764904907/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/bin/mosdepth'�[0m
2024-06-07T12:58:45.6170790Z 12:58:36 �[32mBIOCONDA INFO�[0m (ERR)   Reason: tried: '/usr/local/miniconda/envs/bioconda/conda-bld/d4binding_1646531208915/work/target/release/deps/libd4binding.dylib' (no such file), '/usr/local/lib/libd4binding.dylib' (no such file), '/usr/lib/libd4binding.dylib' (no such file)�[0m

I have the feeling this error is related to brentp/mosdepth#232