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Replace find -printf, which does not exist on macOS #18

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Replace find -printf, which does not exist on macOS #18

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12 changes: 10 additions & 2 deletions scripts/umgap-analyse.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -99,6 +99,15 @@ getconfigdir() {
fi
}

# List the entries of the configuration directory, name only. find's -printf is a
# GNU extension and is not available on the BSD find shipped with macOS.
list_versions() {
for entry in "$(getconfigdir)"/*; do
[ -e "$entry" ] || [ -L "$entry" ] || continue
basename "$entry"
done | sort -n
}

# =========================================================================== #
# Environmental checks.
# =========================================================================== #
Expand Down Expand Up @@ -235,8 +244,7 @@ umgap-setup again."
fi
fi

versions="$(find -H "$(getconfigdir)" -mindepth 1 -maxdepth 1 \
-printf '%P\n' | sort -n)"
versions="$(list_versions)"
for candidate in $versions; do
[ ! -h "$(getconfigdir)/$candidate/taxons.tsv" ] && continue
[ "$tryptic_used" = "true" -a ! -h "$(getconfigdir)/$candidate/tryptic.fst" ] && continue
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12 changes: 10 additions & 2 deletions scripts/umgap-visualize.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,15 @@ getconfigdir() {
fi
}

# List the entries of the configuration directory, name only. find's -printf is a
# GNU extension and is not available on the BSD find shipped with macOS.
list_versions() {
for entry in "$(getconfigdir)"/*; do
[ -e "$entry" ] || [ -L "$entry" ] || continue
basename "$entry"
done | sort -n
}

# =========================================================================== #
# Argument parsing.
# =========================================================================== #
Expand Down Expand Up @@ -105,8 +114,7 @@ fi

debug "checking if we have a taxons file for the frequency table"
if [ "$type" = "csv" ]; then
versions="$(find -H "$(getconfigdir)" -mindepth 1 -maxdepth 1 \
-printf '%P\n' | sort -n)"
versions="$(list_versions)"
for candidate in $versions; do
[ ! -h "$(getconfigdir)/$candidate/taxons.tsv" ] && continue
version="$candidate"
Expand Down
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