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drompa command test fails #44645

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descostesn opened this issue Dec 5, 2023 · 2 comments
Open

drompa command test fails #44645

descostesn opened this issue Dec 5, 2023 · 2 comments

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@descostesn
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Hi,

I am testing locally the following recipe (meta.yaml) with the command bioconda-utils build --git-range master --packages drompa:

{% set version = "3.7.2" %}

package:
  name: drompa3
  version: {{ version }}


source:
  url: https://github.com/rnakato/DROMPA3/archive/refs/tags/v{{version}}.tar.gz
  sha256: 48aa8a5144e190b92e1c2c53c7782723584d8e923f563a58cc2beec08822fb94

requirements:
  build:
    - {{ compiler('c') }}
    - make
  host:
    - gtk2
    - gsl
    - samtools
    - zlib
    - r-base

test:
  commands:
    - parse2wig

about:
  home: https://github.com/rnakato/DROMPA3
  license: GNU General Public License v2.0
  summary: DROMPA can be used for multiple analyses of ChIP-seq data

However, it does not manage to find the command parse2wig. I am wondering if this is because the uncompressed file is in uppercase DROMPA3-3.7.2 ? The linting tells me however that I cannot use an uppercase package name.

I have also tested the building with and without the following build.sh:

#!/bin/bash                                                                                                                                                

git clone git@github.com:coherentgraphics/cpdf-binaries.git

export PATH=$PATH:$HOME/DROMPA3-3.7.2:$HOME/cpdf-binaries/Linux-Intel-64bit/

Any help will be greatly appreciated. Thanks.
@mfansler
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The build.sh needs to do something more along the lines of

#!/bin/bash

## let Conda provide `CC` variable; 
sed -ie /^CC/d Makefile

## connect extra paths to Makefile
## see: https://github.com/rnakato/DROMPA3/blob/master/Makefile
CFLAGS="${CFLAGS} -I${PREFIX}/include/cairo -I${PREFIX}/include/gtk-2.0/gtk"
LIBS="${LIBS} ${LDFLAGS}"

## compile the binaries
make parse2wig drompa_peakcall

## transfer the binaries to prefix
cp parse2wig drompa_peakcall ${PREFIX}/bin/

I left out drompa_draw because that needs the GIO library, which I'm not sure is packaged for Conda.

@descostesn
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Thank you so much for your kind help!

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@mfansler @descostesn