Set pipefail in setup scripts

This was added in places where it's been necessary. Setting it in shared
setup scripts simplifies tests and allows future tests to use pipes
without the need to set pipefail explicitly.

A couple calls with non-zero exit codes have been exposed. These still
fall under expected behavior.

tests/functional/_setup.sh

@@ -1,2 +1,3 @@
 pushd "$TESTDIR" > /dev/null
 export AUGUR="${AUGUR:-../../bin/augur}"
+set -o pipefail

tests/functional/ancestral/cram/_setup.sh

@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail

tests/functional/curate/cram/_setup.sh

@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail

tests/functional/curate/cram/validate-records.t

@@ -25,7 +25,6 @@ error when it encounters the record with mismatched fields.
 Passing the records through multiple augur curate commands should raise the
 same error when it encounters the record with mismatched fields.
 
-  $ set -o pipefail
   $ cat records.ndjson \
   >   | ${AUGUR} curate passthru \
   >   | ${AUGUR} curate passthru \

tests/functional/export_v2/cram/_setup.sh

@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail

tests/functional/filter/cram/_setup.sh

@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail

tests/functional/filter/cram/filter-mismatched-sequences-error.t

@@ -39,6 +39,7 @@ Repeat with sequence and strain outputs. We should get the same results.
   \s*0 .* (re)
   $ grep "^>" filtered.fasta | wc -l
   \s*0 (re)
+  [1]
 
 Repeat without any sequence-based filters.
 Since we expect metadata to be filtered by presence of strains in input sequences, this should produce no results because the intersection of metadata and sequences is empty.

tests/functional/frequencies/cram/_setup.sh

@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail

tests/functional/merge/cram/_setup.sh

@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail

tests/functional/merge/cram/merge.t

@@ -1,7 +1,6 @@
 SETUP
 
   $ source "$TESTDIR"/_setup.sh
-  $ set -o pipefail
 
 
 BASIC USAGE

tests/functional/parse.t

@@ -106,6 +106,7 @@ This should use the first field as the id field and the metadata should not have
   - strain\tvirus\taccession\tdate\tregion\tcountry\tdivision\tcity\tdb\tsegment\tauthors\turl\ttitle\tjournal\tpaper_url (esc)
   ---
   + col1\tvirus\tcol3\tdate\tregion\tcountry\tdivision\tcity\tdb\tsegment\tauthors\turl\ttitle\tjournal\tpaper_url (esc)
+  [1]
   $ rm -f "$TMP/sequences.fasta" "$TMP/metadata.tsv"
 
 Parse compressed Zika sequences into sequences and metadata.

tests/functional/refine/cram/_setup.sh

@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail

tests/functional/titers/cram/_setup.sh

@@ -1,2 +1,3 @@
 pushd "$TESTDIR" > /dev/null
 export AUGUR="${AUGUR:-../../../../bin/augur}"
+set -o pipefail

tests/functional/translate/cram/_setup.sh

@@ -1,2 +1,3 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
 export SCRIPTS="$TESTDIR/../../../../scripts"
+set -o pipefail

tests/functional/tree/cram/_setup.sh

@@ -1 +1,2 @@
 export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}"
+set -o pipefail