Fix permissions

bin/run_hic_tools_pre.sh

@@ -0,0 +1,31 @@
+#!/usr/bin/env bash
+
+# Copyright (C) 2024 Roberto Rossini <roberros@uio.no>
+#
+# SPDX-License-Identifier: MIT
+
+if [ $# -ne 7 ]; then
+  2>&1 echo "Usage:   $0 path_to_pairs path_to_output tmpdir hic_tools.jar resolution cpus memory"
+  2>&1 echo "Example: $0 pairs.4dn.gz out.hic tmp/ hic_tools.jar 1000000 16 650G"
+  exit 1
+fi
+
+path_to_pairs="$1"
+path_to_output="$2"
+tmpdir="$(mktemp -d -t "$3/hictk-tmp-XXXXXXXXXX")"
+hic_tools_jar="$4"
+resolution="$5"
+cpus="$6"
+memory="$7"
+
+
+trap 'rm -rf -- "$tmpdir"' EXIT
+
+java -jar -"Xmx${memory}" "$hic_tools_jar" \
+    pre "$path_to_pairs" "$path_to_output" \
+    hg38 \
+    -r "$resolution" \
+    -n \
+    -t "$tmpdir" \
+    -j "$cpus" \
+    --threads "$cpus"