Update masurca: adding missing dependencies (#64293)

* adding missing dependencies

* python

* pin c_stdlib and openssl to try resolve hash mismatch

* remove conda_build_config.yaml to check if the hash mismatch problem gets resolved

* adding conda_build_config.yaml back

* remove {{ stdlib(c) }} originally added due to linting error

* adding skip-lints due to hash problems

* fix hardcoded perl shebangs to use env

* adding gzip to run dependencies

* adding coreutils to run dependencies

Author: LiaOb21

recipes/masurca/build.sh

@@ -47,3 +47,5 @@ ${BINDIR}/masurca -g masurca_config_example.txt
 cd ${SRC_DIR}/Flye
 make -j"${CPU_COUNT}"
 install -v -m 0755 bin/flye* "${PREFIX}/bin"
+
+find "${PREFIX}/bin" -name "*.pl" -exec sed -i '1s|^#!.*perl.*|#!/usr/bin/env perl|' {} +

recipes/masurca/meta.yaml

@@ -12,7 +12,7 @@ source:
     - 0002-48bit_iterator.patch
 
 build:
-  number: 0
+  number: 1
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}
@@ -22,6 +22,7 @@ requirements:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - make
+    - cmake
     - automake
     - autoconf
     - libtool
@@ -31,11 +32,19 @@ requirements:
     - bzip2
     - libxcrypt
     - boost-cpp
+    - xz
+    - ncurses
+    - openssl
+    - gdbm
   run:
     - boost-cpp
     - perl
+    - python
     - grep
     - bwa
+    - file
+    - gzip
+    - coreutils
 
 test:
   commands:
@@ -58,3 +67,5 @@ extra:
   identifiers:
     - biotools:masurca
     - doi:10.1093/bioinformatics/btt476
+  skip-lints:
+    - compiler_needs_stdlib_c  # until https://github.com/bioconda/bioconda-utils/issues/1095 is resolved