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Fix shellcheck warning and use shellcheck in travis to make sure it c…

…rashes there
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milot-mirdita committed Aug 13, 2019
1 parent d573716 commit 57c994c384b7024ec82a36edbeb75daea9ad8f64
Showing with 7 additions and 0 deletions.
  1. +6 −0 .travis.yml
  2. +1 −0 data/cascaded_clustering.sh
@@ -24,6 +24,7 @@ matrix:
- zlib1g-dev
- libbz2-dev
- vim-common
- shellcheck
env: CC=clang-3.6 CXX=clang++-3.6
- os: linux
dist: trusty
@@ -41,6 +42,7 @@ matrix:
- zlib1g-dev
- libbz2-dev
- vim-common
- shellcheck
env: CC=clang-7 CXX=clang++-7
- os: linux
dist: trusty
@@ -54,6 +56,7 @@ matrix:
- zlib1g-dev
- libbz2-dev
- vim-common
- shellcheck
env: CC=gcc-4.8 CXX=g++-4.8
- os: linux
dist: trusty
@@ -69,6 +72,7 @@ matrix:
- zlib1g-dev
- libbz2-dev
- vim-common
- shellcheck
env: CC=gcc-8 CXX=g++-8
- os: linux
dist: trusty
@@ -85,6 +89,7 @@ matrix:
- libbz2-dev
- vim-common
- libopenmpi-dev
- shellcheck
env: MPI=1 CC=gcc-8 CXX=g++-8
- os: osx
osx_image: xcode10.1
@@ -96,6 +101,7 @@ matrix:
- gcc@8
- zlib
- bzip2
- shellcheck
env: CC=gcc-8 CXX=g++-8
allow_failures:
- env: QEMU_ARM=1
@@ -182,6 +182,7 @@ if [ -n "$REASSIGN" ]; then
fi

if notExists "${TMP_PATH}/missing.single.seqs.db.dbtype"; then
# shellcheck disable=SC2086
"$MMSEQS" prefixid "${TMP_PATH}/clu_accepted_plus_wrong" "${TMP_PATH}/clu_accepted_plus_wrong.tsv" --tsv 1 ${THREADSANDCOMPRESS}
awk 'FNR==NR{f[$2]=1; next} !($1 in f){print $1"\t"$1}' "${TMP_PATH}/clu_accepted_plus_wrong.tsv" "${SOURCE}.index" > "${TMP_PATH}/missing.single.seqs"
# shellcheck disable=SC2086

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