use mktemp in conda-update script, refactor out into contrib and have…

… post-merge and post-checkout call the script

contrib/post-checkout

@@ -1,26 +1,3 @@
 #!/bin/bash
 
-function cmd_exists() {
-    if hash $@ 2> /dev/null ; then
-        return 0
-    else
-        return 1
-    fi
-}
-
-# if conda is available
-if cmd_exists "conda"; then
-    # if a conda environment is active
-    if [ ! -z "$CONDA_DEFAULT_ENV" ]; then
-        # update the conda environment to install the requirements specified
-        if [ "$(uname)" == "Darwin" ]; then
-            # some conda packages dont exist on OSX
-            cat requirements-conda.txt | grep -v kraken > /tmp/requirements-conda.txt
-        else
-            # for linux, just use requirements-conda as-is
-            cp requirements-conda.txt /tmp/requirements-conda.txt
-        fi
-
-        conda install -y -c bioconda --file /tmp/requirements-conda.txt
-    fi
-fi
+./contrib/update-conda-env.sh

contrib/post-merge

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+./contrib/update-conda-env.sh

contrib/update-conda-env.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+
+function cmd_exists() {
+    if hash $@ 2> /dev/null ; then
+        return 0
+    else
+        return 1
+    fi
+}
+
+requirements_file="$(mktemp -t requirements-conda.txt)"
+
+# if conda is available
+if cmd_exists "conda"; then
+    # if a conda environment is active
+    if [ ! -z "$CONDA_DEFAULT_ENV" ]; then
+        # update the conda environment to install the requirements specified
+        if [ "$(uname)" == "Darwin" ]; then
+            # some conda packages dont exist on OSX
+            cat requirements-conda.txt | grep -v kraken > "$requirements_file"
+        else
+            # for linux, just use requirements-conda as-is
+            cp requirements-conda.txt "$requirements_file"
+        fi
+
+        conda install -y -c bioconda --file "$requirements_file"
+        rm "$requirements_file"
+    fi
+fi