update ucsc-bedclip adding new platform (#46626)

* update ucsc-bedclip adding new platform * add patch * fix compilation for arm * remove from blacklist * try another way to specify compiler version * edit pin_subpackage --------- Co-authored-by: Joshua Zhuang <[email protected]>
bioconda · Mar 22, 2024 · 9985819 · 9985819
1 parent b0ad8e8
commit 9985819
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Showing 5 changed files with 40 additions and 4 deletions.
diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -802,7 +802,6 @@ recipes/ucsc-axtsort
 recipes/ucsc-axtswap
 recipes/ucsc-axttomaf
 recipes/ucsc-bamtopsl
-recipes/ucsc-bedclip
 recipes/ucsc-bedcommonregions
 recipes/ucsc-bedcoverage
 recipes/ucsc-bedextendranges

diff --git a/recipes/ucsc-bedclip/build.sh b/recipes/ucsc-bedclip/build.sh
@@ -1,8 +1,17 @@
 #!/bin/bash
-mkdir -p "$PREFIX/bin"
-export MACHTYPE=x86_64
+
+if [ $(arch) = "aarch64" ]
+then
+    export CFLAGS+=" -O3 -mcpu=neoverse-n1 "
+    export CPPFLAGS+=" -O3 -mcpu=neoverse-n1 "
+else
+    export MACHTYPE=x86_64
+fi
+
 export BINDIR=$(pwd)/bin
 export L="${LDFLAGS}"
+
+mkdir -p "$PREFIX/bin"
 mkdir -p "$BINDIR"
 (cd kent/src/lib && make)
 (cd kent/src/htslib && make)

diff --git a/recipes/ucsc-bedclip/conda_build_config.yaml b/recipes/ucsc-bedclip/conda_build_config.yaml
@@ -0,0 +1,2 @@
+c_compiler_version:
+  - 8
diff --git a/recipes/ucsc-bedclip/meta.yaml b/recipes/ucsc-bedclip/meta.yaml
@@ -12,10 +12,13 @@ source:
   sha256: "{{ sha256 }}"
   patches:
     - "include.patch"
+    - "patch1.patch"
 
 build:
   skip: True  # [osx]
-  number: 2
+  number: 3
+  run_exports:
+    - {{ pin_subpackage("ucsc-bedclip", max_pin=None) }}
 
 requirements:
   build:
@@ -40,6 +43,10 @@ test:
     # just check for existence, because the individual packages have no unified behavior
     - which {{ program }}
 
+extra:
+  additional-platforms:
+    - linux-aarch64
+
 about:
   home: "http://hgdownload.cse.ucsc.edu/admin/exe/"
   license: "varies; see http://genome.ucsc.edu/license"

diff --git a/recipes/ucsc-bedclip/patch1.patch b/recipes/ucsc-bedclip/patch1.patch
@@ -0,0 +1,19 @@
+--- userApps/kent/src/lib/htmshell.c.old	2022-10-28 08:32:08.344445121 +0000
++++ userApps/kent/src/lib/htmshell.c	2022-10-28 08:32:31.708262420 +0000
+@@ -711,11 +711,11 @@
+ puts("Status: 400\r");
+ puts("Content-Type: text/plain; charset=UTF-8\r");
+ puts("\r");
+-if (format != NULL && args != NULL)
+-    {
+-    vfprintf(stdout, format, args);
+-    fprintf(stdout, "\n");
+-    }
++if (format != NULL)
++    {
++    vfprintf(stdout, format, args);
++    fprintf(stdout, "\n");
++    }
+ exit(-1);
+ }
+