UCSC blacklist

build-fail-blacklist

@@ -885,6 +885,20 @@ recipes/bioconductor-snapcgh
 recipes/bioconductor-italics
 recipes/bioconductor-biggr
 
+# stringify can't find libmysqlclient.18
+recipes/ucsc-overlapselect
+recipes/ucsc-pslmap
+recipes/ucsc-pslcdnafilter
+
+# can't open output file for writing
+recipes/ucsc-bedtogenepred
+
+# cp: No such file or directory (OSX only)
+recipes/ucsc-fetchchromsizes
+recipes/ucsc-bedjointaboffset
+recipes/ucsc-expmatrixtobarchartbed
+recipes/ucsc-websync
+
 # Unknown java error
 recipes/bioconductor-msgfplus
-recipes/bioconductor-msgfgui
+recipes/bioconductor-msgfgui

recipes/ucsc-addcols/build.sh

@@ -1,16 +1,12 @@
 #!/bin/bash
 mkdir -p "$PREFIX/bin"
-if [ "$(uname)" == "Darwin" ]; then
-    cp addCols "$PREFIX/bin"
-else
-    export MACHTYPE=x86_64
-    export BINDIR=$(pwd)/bin
-    mkdir -p "$BINDIR"
-    (cd kent/src/lib && make)
-    (cd kent/src/htslib && make)
-    (cd kent/src/jkOwnLib && make)
-    (cd kent/src/hg/lib && make)
-    (cd kent/src/utils/addCols && make)
-    cp bin/addCols "$PREFIX/bin"
-fi
+export MACHTYPE=x86_64
+export BINDIR=$(pwd)/bin
+mkdir -p "$BINDIR"
+(cd kent/src/lib && make)
+(cd kent/src/htslib && make)
+(cd kent/src/jkOwnLib && make)
+(cd kent/src/hg/lib && make)
+(cd kent/src/utils/addCols && make)
+cp bin/addCols "$PREFIX/bin"
 chmod +x "$PREFIX/bin/addCols"

recipes/ucsc-addcols/meta.yaml

@@ -1,38 +1,36 @@
 {% set package = "ucsc-addcols" %}
 {% set program = "addCols" %}
-{% set version = "366" %}
-{% set sha256 = "c110a27acd25df5c4ae56a9d4c359b40e83e3b1cca7cb61361e623fc8574bdd7" %}
+{% set version = "377" %}
+{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %}
 
 package:
   name: "{{ package }}"
   version: "{{ version }}"
 
 source:
-  url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v{{ version }}.src.tgz"                      # [linux]
-  sha256: "{{ sha256 }}"                                                    # [linux]
-  patches:                                                                                   # [linux]
-    - "include.patch"                                                                        # [linux]
-
-  url: "http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/{{ program }}"                    # [osx]
+  url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v{{ version }}.src.tgz"
+  sha256: "{{ sha256 }}"
+  patches:
+    - "include.patch"
 
 build:
   number: 0
 
 requirements:
   build:
-    - {{ compiler('c') }}                                       # [linux]
+    - {{ compiler('c') }}
   host:
-    - libpng                                                    # [linux]
-    - libuuid                                                   # [linux]
-    - mysql-connector-c                                         # [linux]
-    - openssl                                                   # [linux]
+    - libpng
+    - libuuid
+    - mysql-connector-c
+    - openssl
     - zlib
 
   run:
-    - libpng                                                    # [linux]
-    - libuuid                                                   # [linux]
-    - mysql-connector-c                                         # [linux]
-    - openssl                                                   # [linux]
+    - libpng
+    - libuuid
+    - mysql-connector-c
+    - openssl
     - zlib
 
 test:
@@ -44,7 +42,3 @@ about:
   home: "http://hgdownload.cse.ucsc.edu/admin/exe/"
   license: "varies; see http://genome.ucsc.edu/license"
   summary: "Sum columns in a text file."
-
-extra:
-  skip-lints:
-    - missing_hash

recipes/ucsc-ameme/build.sh

@@ -1,16 +1,12 @@
 #!/bin/bash
 mkdir -p "$PREFIX/bin"
-if [ "$(uname)" == "Darwin" ]; then
-    cp ameme "$PREFIX/bin"
-else
-    export MACHTYPE=x86_64
-    export BINDIR=$(pwd)/bin
-    mkdir -p "$BINDIR"
-    (cd kent/src/lib && make)
-    (cd kent/src/htslib && make)
-    (cd kent/src/jkOwnLib && make)
-    (cd kent/src/hg/lib && make)
-    (cd kent/src/ameme && make)
-    cp bin/ameme "$PREFIX/bin"
-fi
+export MACHTYPE=x86_64
+export BINDIR=$(pwd)/bin
+mkdir -p "$BINDIR"
+(cd kent/src/lib && make)
+(cd kent/src/htslib && make)
+(cd kent/src/jkOwnLib && make)
+(cd kent/src/hg/lib && make)
+(cd kent/src/ameme && make)
+cp bin/ameme "$PREFIX/bin"
 chmod +x "$PREFIX/bin/ameme"

recipes/ucsc-ameme/meta.yaml

@@ -1,38 +1,36 @@
 {% set package = "ucsc-ameme" %}
 {% set program = "ameme" %}
-{% set version = "366" %}
-{% set sha256 = "c110a27acd25df5c4ae56a9d4c359b40e83e3b1cca7cb61361e623fc8574bdd7" %}
+{% set version = "377" %}
+{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %}
 
 package:
   name: "{{ package }}"
   version: "{{ version }}"
 
 source:
-  url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v{{ version }}.src.tgz"                      # [linux]
-  sha256: "{{ sha256 }}"                                                    # [linux]
-  patches:                                                                                   # [linux]
-    - "include.patch"                                                                        # [linux]
-
-  url: "http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/{{ program }}"                    # [osx]
+  url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v{{ version }}.src.tgz"
+  sha256: "{{ sha256 }}"
+  patches:
+    - "include.patch"
 
 build:
   number: 0
 
 requirements:
   build:
-    - {{ compiler('c') }}                                       # [linux]
+    - {{ compiler('c') }}
   host:
-    - libpng                                                    # [linux]
-    - libuuid                                                   # [linux]
-    - mysql-connector-c                                         # [linux]
-    - openssl                                                   # [linux]
+    - libpng
+    - libuuid
+    - mysql-connector-c
+    - openssl
     - zlib
 
   run:
-    - libpng                                                    # [linux]
-    - libuuid                                                   # [linux]
-    - mysql-connector-c                                         # [linux]
-    - openssl                                                   # [linux]
+    - libpng
+    - libuuid
+    - mysql-connector-c
+    - openssl
     - zlib
 
 test:
@@ -44,7 +42,3 @@ about:
   home: "http://hgdownload.cse.ucsc.edu/admin/exe/"
   license: "varies; see http://genome.ucsc.edu/license"
   summary: "find common patterns in DNA"
-
-extra:
-  skip-lints:
-    - missing_hash

recipes/ucsc-autodtd/build.sh

@@ -1,16 +1,12 @@
 #!/bin/bash
 mkdir -p "$PREFIX/bin"
-if [ "$(uname)" == "Darwin" ]; then
-    cp autoDtd "$PREFIX/bin"
-else
-    export MACHTYPE=x86_64
-    export BINDIR=$(pwd)/bin
-    mkdir -p "$BINDIR"
-    (cd kent/src/lib && make)
-    (cd kent/src/htslib && make)
-    (cd kent/src/jkOwnLib && make)
-    (cd kent/src/hg/lib && make)
-    (cd kent/src/hg/autoDtd && make)
-    cp bin/autoDtd "$PREFIX/bin"
-fi
+export MACHTYPE=x86_64
+export BINDIR=$(pwd)/bin
+mkdir -p "$BINDIR"
+(cd kent/src/lib && make)
+(cd kent/src/htslib && make)
+(cd kent/src/jkOwnLib && make)
+(cd kent/src/hg/lib && make)
+(cd kent/src/hg/autoDtd && make)
+cp bin/autoDtd "$PREFIX/bin"
 chmod +x "$PREFIX/bin/autoDtd"

recipes/ucsc-autodtd/meta.yaml

@@ -1,38 +1,36 @@
 {% set package = "ucsc-autodtd" %}
 {% set program = "autoDtd" %}
-{% set version = "366" %}
-{% set sha256 = "c110a27acd25df5c4ae56a9d4c359b40e83e3b1cca7cb61361e623fc8574bdd7" %}
+{% set version = "377" %}
+{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %}
 
 package:
   name: "{{ package }}"
   version: "{{ version }}"
 
 source:
-  url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v{{ version }}.src.tgz"                      # [linux]
-  sha256: "{{ sha256 }}"                                                    # [linux]
-  patches:                                                                                   # [linux]
-    - "include.patch"                                                                        # [linux]
-
-  url: "http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/{{ program }}"                    # [osx]
+  url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v{{ version }}.src.tgz"
+  sha256: "{{ sha256 }}"
+  patches:
+    - "include.patch"
 
 build:
   number: 0
 
 requirements:
   build:
-    - {{ compiler('c') }}                                       # [linux]
+    - {{ compiler('c') }}
   host:
-    - libpng                                                    # [linux]
-    - libuuid                                                   # [linux]
-    - mysql-connector-c                                         # [linux]
-    - openssl                                                   # [linux]
+    - libpng
+    - libuuid
+    - mysql-connector-c
+    - openssl
     - zlib
 
   run:
-    - libpng                                                    # [linux]
-    - libuuid                                                   # [linux]
-    - mysql-connector-c                                         # [linux]
-    - openssl                                                   # [linux]
+    - libpng
+    - libuuid
+    - mysql-connector-c
+    - openssl
     - zlib
 
 test:
@@ -44,7 +42,3 @@ about:
   home: "http://hgdownload.cse.ucsc.edu/admin/exe/"
   license: "varies; see http://genome.ucsc.edu/license"
   summary: "Give this a XML document to look at and it will come up with a DTD"
-
-extra:
-  skip-lints:
-    - missing_hash

recipes/ucsc-autosql/build.sh

@@ -1,16 +1,12 @@
 #!/bin/bash
 mkdir -p "$PREFIX/bin"
-if [ "$(uname)" == "Darwin" ]; then
-    cp autoSql "$PREFIX/bin"
-else
-    export MACHTYPE=x86_64
-    export BINDIR=$(pwd)/bin
-    mkdir -p "$BINDIR"
-    (cd kent/src/lib && make)
-    (cd kent/src/htslib && make)
-    (cd kent/src/jkOwnLib && make)
-    (cd kent/src/hg/lib && make)
-    (cd kent/src/hg/autoSql && make)
-    cp bin/autoSql "$PREFIX/bin"
-fi
+export MACHTYPE=x86_64
+export BINDIR=$(pwd)/bin
+mkdir -p "$BINDIR"
+(cd kent/src/lib && make)
+(cd kent/src/htslib && make)
+(cd kent/src/jkOwnLib && make)
+(cd kent/src/hg/lib && make)
+(cd kent/src/hg/autoSql && make)
+cp bin/autoSql "$PREFIX/bin"
 chmod +x "$PREFIX/bin/autoSql"

recipes/ucsc-autosql/meta.yaml

@@ -1,38 +1,36 @@
 {% set package = "ucsc-autosql" %}
 {% set program = "autoSql" %}
-{% set version = "366" %}
-{% set sha256 = "c110a27acd25df5c4ae56a9d4c359b40e83e3b1cca7cb61361e623fc8574bdd7" %}
+{% set version = "377" %}
+{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %}
 
 package:
   name: "{{ package }}"
   version: "{{ version }}"
 
 source:
-  url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v{{ version }}.src.tgz"                      # [linux]
-  sha256: "{{ sha256 }}"                                                    # [linux]
-  patches:                                                                                   # [linux]
-    - "include.patch"                                                                        # [linux]
-
-  url: "http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/{{ program }}"                    # [osx]
+  url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.v{{ version }}.src.tgz"
+  sha256: "{{ sha256 }}"
+  patches:
+    - "include.patch"
 
 build:
   number: 0
 
 requirements:
   build:
-    - {{ compiler('c') }}                                       # [linux]
+    - {{ compiler('c') }}
   host:
-    - libpng                                                    # [linux]
-    - libuuid                                                   # [linux]
-    - mysql-connector-c                                         # [linux]
-    - openssl                                                   # [linux]
+    - libpng
+    - libuuid
+    - mysql-connector-c
+    - openssl
     - zlib
 
   run:
-    - libpng                                                    # [linux]
-    - libuuid                                                   # [linux]
-    - mysql-connector-c                                         # [linux]
-    - openssl                                                   # [linux]
+    - libpng
+    - libuuid
+    - mysql-connector-c
+    - openssl
     - zlib
 
 test:
@@ -44,7 +42,3 @@ about:
   home: "http://hgdownload.cse.ucsc.edu/admin/exe/"
   license: "varies; see http://genome.ucsc.edu/license"
   summary: "create SQL and C code for permanently storing"
-
-extra:
-  skip-lints:
-    - missing_hash