[ci skip] Merge PR 25932

Merge PR #25932, commits were: * Add [de]activate scripts to workaround cbcrg/tcoffee#27 * Skip osx Just running `t_coffee` fails with: ``` 04:33:21 BIOCONDA INFO (OUT) -max_n_proc D [0] 1 04:33:21 BIOCONDA INFO (OUT) 04:33:21 BIOCONDA INFO (OUT) 04:33:21 BIOCONDA INFO (OUT) ************************************************************************************************* 04:33:21 BIOCONDA INFO (OUT) * FULL TRACE BACK PID: 2901 04:33:21 BIOCONDA INFO (OUT) 2901 -- ERROR: COREDUMP: T-COFFEE Version_13.45.32.7d81f5b (2020-12-18 11:45:26 - Revision 7d7e789 - Build 647) 04:33:21 BIOCONDA INFO (OUT) ************************************************************************************************* 04:33:21 BIOCONDA INFO (OUT) 04:33:21 BIOCONDA INFO (OUT) ****************************************************************** 04:33:21 BIOCONDA INFO (OUT) * Abnormal Termination 04:33:21 BIOCONDA INFO (OUT) * Job NOT Completed:[T-COFFEE, Version_13.45.32.7d81f5b] 04:33:21 BIOCONDA INFO (OUT) * Please CHECK: 04:33:21 BIOCONDA INFO (OUT) * -1 The format of your Input Files 04:33:21 BIOCONDA INFO (OUT) * -2 The parameters 04:33:21 BIOCONDA INFO (OUT) * -3 The use of special characters in sequence names: 04:33:21 BIOCONDA INFO (OUT) * (@, |, %...) 04:33:21 BIOCONDA INFO (OUT) * -4 The Online Doc (http://www.tcoffee.org) 04:33:21 BIOCONDA INFO (OUT) * -5 re-run your CL (see below) with the -debug option. This will produce a debug file you can send us. 04:33:21 BIOCONDA INFO (OUT) * 04:33:21 BIOCONDA INFO (OUT) * NO 04:33:21 BIOCONDA INFO (OUT) * to: 04:33:21 BIOCONDA INFO (OUT) * [email protected] 04:33:21 BIOCONDA INFO (OUT) * If you run T-Coffee over the WEB: 04:33:21 BIOCONDA INFO (OUT) * Windows Cut and Paste is sometimes erratic and 04:33:21 BIOCONDA INFO (OUT) * it can loose carriage returns. If you suspect this, 04:33:21 BIOCONDA INFO (OUT) * try to cut and paste through an intermediate application 04:33:21 BIOCONDA INFO (OUT) * (word pad) and inspect the results 04:33:21 BIOCONDA INFO (OUT) 04:33:21 BIOCONDA INFO (OUT) 04:33:21 BIOCONDA INFO (OUT) * CONFIDENTIALITY: 04:33:21 BIOCONDA INFO (OUT) * The File NO may contain your personal DATA 04:33:21 BIOCONDA INFO (OUT) * Remove ALL confidential DATA from this file BEFORE sending it 04:33:21 BIOCONDA INFO (OUT) ****************************************************************** 04:33:21 BIOCONDA INFO (OUT) # Command Line: t_coffee [PROGRAM:T-COFFEE] 04:33:21 BIOCONDA INFO (OUT) 04:33:21 BIOCONDA INFO (OUT) # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 2901 ppid 2895 04:33:21 BIOCONDA INFO (OUT) #CL: t_coffee ``` * Update t-coffee to 13.45.0.4846264
bioconda · Dec 23, 2020 · 47c10bb · 47c10bb
1 parent ffccc76
commit 47c10bb
Show file tree

Hide file tree

Showing 4 changed files with 26 additions and 10 deletions.
diff --git a/recipes/t-coffee/activate.sh b/recipes/t-coffee/activate.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+export MAX_N_PID_4_TCOFFEE=$(cat /proc/sys/kernel/pid_max)
diff --git a/recipes/t-coffee/build.sh b/recipes/t-coffee/build.sh
@@ -15,3 +15,11 @@ make CC=$CXX CFLAGS="$CFLAGS"
 # install tcoffee in the target bin directory 
 mkdir -p $PREFIX/bin
 cp t_coffee $PREFIX/bin
+
+# Copy the [de]activate scripts to $PREFIX/etc/conda/[de]activate.d.
+# This will allow them to be run on environment activation.
+for CHANGE in "activate" "deactivate"
+do
+    mkdir -p "${PREFIX}/etc/conda/${CHANGE}.d"
+    cp "${RECIPE_DIR}/${CHANGE}.sh" "${PREFIX}/etc/conda/${CHANGE}.d/${PKG_NAME}_${CHANGE}.sh"
+done
diff --git a/recipes/t-coffee/deactivate.sh b/recipes/t-coffee/deactivate.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+unset MAX_N_PID_4_TCOFFEE
diff --git a/recipes/t-coffee/meta.yaml b/recipes/t-coffee/meta.yaml
@@ -1,15 +1,18 @@
-{% set version = "13.39.0.d675aed" %}
+{% set version = "13.45.0.4846264" %}
 
 package:
   name: t-coffee
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
+  skip: True  # [osx]
 
 source:
-  url: http://tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution_Version_{{ version }}.tar.gz
-  sha256: 33e0eb17fe5a88e59ddeaad2e54782e3ab5b2f70d8654e54aff1ccc4e5cc127f
+  # The latest stable release is at http://www.tcoffee.org/Packages/Stable/Latest/ ,
+  # but is then archived at http://www.tcoffee.org/Packages/Archives/
+  url: http://www.tcoffee.org/Packages/Archives/T-COFFEE_distribution_Version_{{ version }}.tar.gz
+  sha256: c8e5ba17de11ddf07cf2ed37f077d81c1432d55b77761f115f9374de6f8d0d03
 
 requirements:
   build:
@@ -19,26 +22,27 @@ requirements:
     - blast
     - clustalo
     - clustalw
+    - consan # [not osx]
     - dca
     - dialign-tx=1.0.2
     - mafft=7.310
     - muscle
     - mustang=3.2.3
+    - pasta
     - poa=2.0 # [not osx]
     - prank
     - phylip
-    - viennarna=2.1.9
-    - consan # [not osx]
-    - pasta
-    - tmalign
     - ruby
+    - tmalign
+    - viennarna=2.1.9
 
 test:
   commands:
-    - HOME=/tmp/ t_coffee -version
+    - HOME=/tmp t_coffee -version
+    - HOME=/tmp t_coffee 2>&1 | grep "mafft is  Installed"
 
 about:
-  home: "https://github.com/cbcrg/tcoffee"
+  home: http://www.tcoffee.org/Projects/tcoffee/
   license: "GPL"
   summary: "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence"
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#!/bin/sh
		export MAX_N_PID_4_TCOFFEE=$(cat /proc/sys/kernel/pid_max)