update requirements, correct env, sanity check

Author: dickgroenenberg

translatenucleotide.py

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
 
 # This script is compatible with Python3
 # Tested with 2to3; no changes made

translatenucleotide.sh

@@ -1,6 +1,13 @@
 #!/bin/bash
-echo "Test text"
-outlocation=$(mktemp -d /media/GalaxyData/database/files/XXXXXX)
+
+# sanity check
+printf "Conda env: $CONDA_DEFAULT_ENV\n"
+printf "Python version: $(python --version)\n"
+printf "Biopython version: $(conda list | egrep biopython | awk '{print $2}')\n"
+printf "Emboss version: $(embossversion 2>&1 | tail -n1)\n"
+printf "Bash version: ${BASH_VERSION}\n\n"
+
+outlocation=$(mktemp -d /data/files/XXXXXX)
 SCRIPTDIR=$(dirname "$(readlink -f "$0")")
 transeq -sequence $1 -frame 6 -outseq $outlocation"/proteintranslation" -table $4 2> /dev/null 
 python $SCRIPTDIR"/translatenucleotide.py" -i $outlocation"/proteintranslation" -o $2 -s $3

translatenucleotide.xml

@@ -6,9 +6,9 @@
 <description>EMBOSS transeq</description>
 -->
 <requirements>
-    <requirement type="package" version="3.7.0">python</requirement>
-	<requirement type="package">biopython</requirement>
 	<requirement type="package" version="6.6.0">emboss</requirement>
+	<requirement type="package" version="3.9.0">python</requirement>
+	<requirement type="package" version="1.79">biopython</requirement>
 </requirements>
 <command>
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