From 957c6af989e3f05fc3e401ee3a3526ae788b573f Mon Sep 17 00:00:00 2001
From: Carl Mathias Kobel <carl.mathias.kobel@nmbu.no>
Date: Sun, 12 May 2024 15:39:27 +0200
Subject: [PATCH] Add Gapseq (#47417)
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* init

* passes bioconda-utils lint

* works too

* polishing

* final test

* ensure correct pinning

* minor tweaks

* test was too long.

* amend

* work on tests after package has been published

* updates according to bgruening's comments

* r-chnosz is now available on conda-forge

* amend

* reset build number

* Update recipes/gapseq/meta.yaml

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 recipes/gapseq/build.sh  | 41 +++++++++++++++++++++++
 recipes/gapseq/meta.yaml | 71 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 112 insertions(+)
 create mode 100644 recipes/gapseq/build.sh
 create mode 100644 recipes/gapseq/meta.yaml

diff --git a/recipes/gapseq/build.sh b/recipes/gapseq/build.sh
new file mode 100644
index 0000000000000..5cf8ec2bdb7b9
--- /dev/null
+++ b/recipes/gapseq/build.sh
@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+
+# Installation instructions taken from https://github.com/jotech/gapseq/blob/master/docs/install.md#conda April 2024 by cmkobel
+
+# Copy contents to conda prefix
+mkdir -p ${PREFIX}/gapseq/
+cp ISSUE_TEMPLATE.MD LICENSE README.md gapseq gapseq_env.yml ${PREFIX}/gapseq/
+cp -r dat/ docs/ src/ toy/ unit/ ${PREFIX}/gapseq/
+
+
+# Installing the CRAN archived sybilSBML package here requires a bunch of debugging to set the lib paths in R. That time is probably better spend fixing the package (sybilSBML) in the first place. So here is a quick workaround that makes this process a bit easier for the user. SybilSBML is not strictly necessary so I think the priority should be to get the main package (gapseq) working first.
+echo '''#!/usr/bin/env bash
+wget https://cran.r-project.org/src/contrib/Archive/sybilSBML/sybilSBML_3.1.2.tar.gz
+R CMD INSTALL --configure-args=" \
+--with-sbml-include=$CONDA_PREFIX/include \
+--with-sbml-lib=$CONDA_PREFIX/lib" sybilSBML_3.1.2.tar.gz
+rm sybilSBML_3.1.2.tar.gz
+''' > ${PREFIX}/gapseq/src/install_archived_sybilSBML.sh
+chmod +x ${PREFIX}/gapseq/src/install_archived_sybilSBML.sh
+# Now the user can "easily" install this after installing the bioconda package with install_archived_sybilSBML.sh (This file will be linked to bin/).
+
+
+# Download reference sequence data
+# To install the database, we must call the installed file as it uses its own path to place the files correctly.
+bash ${PREFIX}/gapseq/src/update_sequences.sh
+
+
+# Final setup - Make binary available
+mkdir -p ${PREFIX}/bin
+ln -sr ${PREFIX}/gapseq/gapseq ${PREFIX}/bin/
+ln -sr ${PREFIX}/gapseq/src/update_sequences.sh ${PREFIX}/bin/
+ln -sr ${PREFIX}/gapseq/src/install_archived_sybilSBML.sh ${PREFIX}/bin/
+
+
+# --- 
+
+
+# Build at home with (before submitting to azure):
+# conda activate bioconda-utils
+# bioconda-utils lint --git-range master
+# bioconda-utils build --mulled-test --git-range master
diff --git a/recipes/gapseq/meta.yaml b/recipes/gapseq/meta.yaml
new file mode 100644
index 0000000000000..b62b67d0b8755
--- /dev/null
+++ b/recipes/gapseq/meta.yaml
@@ -0,0 +1,71 @@
+{% set version = "1.2" %}
+
+package:
+  name: gapseq
+  version: {{ version }}
+
+source:
+  url: https://github.com/jotech/gapseq/archive/refs/tags/v{{ version}}.tar.gz
+  sha256: 061799f8e0406662450dd3d8d61d824220670fb23231895deecd490a5cbdf7cf
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('gapseq', max_pin="x") }}
+  skip: True # [osx]
+
+requirements:
+  run:
+    - r-base
+    - perl
+    - parallel
+    - gawk
+    - sed
+    - grep
+    - bc
+    - git
+    - coreutils
+    - wget
+    - openssl
+    - barrnap
+    - bedtools
+    - exonerate
+    - glpk
+    - hmmer
+    - blast
+    - libsbml 
+    - r-data.table
+    - r-stringr
+    - r-stringi
+    - r-getopt
+    - r-doParallel
+    - r-foreach
+    - r-r.utils
+    - r-sybil
+    - r-biocmanager
+    - bioconductor-biostrings
+    - r-jsonlite
+    - r-renv
+    - r-glpkapi
+    - r-rcurl
+    - r-httr
+    - r-chnosz
+  build: 
+    - wget
+
+test:
+  commands:
+    - gapseq test
+
+about:
+  home: https://github.com/jotech/gapseq
+  summary: Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks 
+  license_family: GPL
+  license: AGPL-3.0-only
+  license_file: LICENSE
+extra:
+  skip-lints:
+    - should_be_noarch_generic
+  recipe-maintainers:
+    - cmkobel
+