From ba3273462b99f8ee7f56ac378ece9ecf2ed2cdaf Mon Sep 17 00:00:00 2001 From: Felix Van der Jeugt Date: Wed, 16 Oct 2019 09:01:34 +0200 Subject: [PATCH] Let users confirm not having a FGS++ --- scripts/umgap-setup.sh | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/scripts/umgap-setup.sh b/scripts/umgap-setup.sh index 7031480..0e3bf6d 100755 --- a/scripts/umgap-setup.sh +++ b/scripts/umgap-setup.sh @@ -1,10 +1,4 @@ #!/bin/sh -# - install rust? or ask to -# - install umgap -# - ask configdir (or use XDG/unipept or ~/.unipept) -# - install FGSpp (or ask to) and find it (symlink in configdir) -# - download taxons (ask location? to XDG_DATA_HOME/unipept) (symlink in configdir) (VERSION!) -# - download indices (ask first: if, where) (symlink in configdir) (VERSION!) # print stuff to stderr and exits with fault crash() { @@ -93,7 +87,9 @@ fi # If FGSpp is found and works, link it in the config directory. if [ -z "$fgsppdir" ]; then - echo 'FragGeneScan++ was not provided, only pipelines not using it will be available.' + if ! yesno 'FragGeneScan++ (-f) was not provided, only pipelines not using it will be available.'; then + crash 'Pass the location of FragGeneScan++ with -f.' + fi else cd "$fgsppdir" if ! printf '>a\nA' | ./FGSpp -s stdin -o stdout -w 0 -t illumina_10 -c 240 > /dev/null; then @@ -168,6 +164,12 @@ if [ "$?" != 0 ]; then fi echo "Latest version is ${version}." +echo +echo 'For any type of analysis, you need a taxonomony. For mapping tryptic or' +echo '9-mer peptides to it, you need the respective index file of the same' +echo 'version.' +echo + # Checking the files for this version. taxons="$DATASERVER/$version/taxons.tsv" if [ -h "$configdir/$version/taxons.tsv" ]; then