pepnovo: add aarch64/arm64 build (#51206)

* pepnovo: add aarch64/arm64 build

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* pepnovo: add patch to fix a compilation error with positive infinity

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

* Add -Wno-register to CXXFLAGS for OSX

Trying to fix:
```
base64.cpp:124:11: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]�[0m
2024-10-08T08:41:28.5270550Z 08:41:27 �[32mBIOCONDA INFO�[0m (ERR)       int register a;�[0m
```

---------

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>

build-fail-blacklist

@@ -179,7 +179,6 @@ recipes/gemma
 recipes/roary
 recipes/deltabs
 recipes/gottcha
-recipes/pepnovo
 recipes/ea-utils
 recipes/nextgenmap
 recipes/igor_vdj

recipes/pepnovo/.gitattributes

@@ -0,0 +1,2 @@
+# the file contains both CRLF and LF line endings. Tell Git to not touch it
+0002-fix-float-positive-infinity.patch binary

recipes/pepnovo/0002-fix-float-positive-infinity.patch

@@ -0,0 +1,29 @@
+--- src/CumulativeSeqProb.h.orig	2024-10-07 12:43:16.904000000 +0000
++++ src/CumulativeSeqProb.h	2024-10-07 12:54:32.420000000 +0000
+@@ -1,21 +1,22 @@
+ #ifndef __CUMULATIVESEQPROB_H__
+ #define __CUMULATIVESEQPROB_H__
+
++#include <math.h>
+ #include "ME_REG.h"
+ #include "Config.h"
+ #include "FileManagement.h"
+
+ struct SeqPath;
+
+-const float qual_levels[]		= {0.10,0.25,0.5,0.75,0.9,0.95,0.98,POS_INF};
++const float qual_levels[]		= {0.10,0.25,0.5,0.75,0.9,0.95,0.98,INFINITY};
+ const int num_qual_levels		= sizeof(qual_levels)/sizeof(float);
+ const int rank_levels[]			= {0,1,2,4,8,16,32,64,128,256,POS_INF}; // at these ranks we fill the 
+ const int num_rank_levels		= sizeof(rank_levels)/sizeof(int);
+-const float rank_score_levels[] = {-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7,POS_INF};
++const float rank_score_levels[] = {-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7,INFINITY};
+ const int num_rank_score_levels = sizeof(rank_score_levels)/sizeof(float);
+-const float pnv_score_levels[]	= {0,10,20,30,40,50,60,70,80,90,100,110,120,130,140,POS_INF};
++const float pnv_score_levels[]	= {0.f,10.f,20.f,30.f,40.f,50.f,60.f,70.f,80.f,90.f,100.f,110.f,120.f,130.f,140.f,INFINITY};
+ const int num_pnv_score_levels	= sizeof(pnv_score_levels)/sizeof(float);
+-const float avg_prob_levels[]	= {0.1,0.25,0.5,0.75,0.9,0.95,POS_INF};
++const float avg_prob_levels[]	= {0.1,0.25,0.5,0.75,0.9,0.95,INFINITY};
+ const int num_avg_prob_levels	= sizeof(avg_prob_levels)/sizeof(float);
+ const int special_ranks[]		= {0,8,128};	// at these ranks we fill the big set of rank score and pnv score features
+ const int num_special_ranks		= sizeof(special_ranks)/sizeof(int);

recipes/pepnovo/build.sh

@@ -1,10 +1,12 @@
 #!/bin/bash
 
+set -xe
+
 cd src/
 
 # Below we add -Wno-narrowing because of the compilation error:
 #   CumulativeSeqProb.h:10:71: error: narrowing conversion of '999999999' from 'int' to 'float' inside { } [-Wnarrowing]
-make CC="${CXX}" CFLAGS="${CXXFLAGS} -Wno-narrowing " LDFLAGS="${LDFLAGS}"
+make -j ${CPU_COUNT} CC="${CXX}" CFLAGS="${CXXFLAGS} -Wno-narrowing -Wno-register " LDFLAGS="${LDFLAGS}"
 
 mkdir -p ${PREFIX}/bin
 cp PepNovo_bin ${PREFIX}/bin/pepnovo

recipes/pepnovo/meta.yaml

@@ -7,9 +7,12 @@ source:
   md5: af2a863487cb53bf0e92f00d395c4f0d
   patches:
     - 0001-fix-type-error-in-ReScoreDB.cpp.patch
+    - 0002-fix-float-positive-infinity.patch
 
 build:
-  number: 3
+  number: 4
+  run_exports:
+    - {{ pin_subpackage('pepnovo', max_pin=None) }}
 
 requirements:
   build:
@@ -28,5 +31,8 @@ about:
   summary: PepNovo serves as a high throughput de novo peptide sequencing tool for tandem mass spectrometry data
 
 extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
   identifiers:
     - biotools:pepnovo