Mercurial > repos > ebi-gxa > fastq_filter_n
annotate get_test_data.sh @ 0:df87d29fac7f draft default tip
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
author | ebi-gxa |
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date | Tue, 15 Feb 2022 16:38:56 +0000 |
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df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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1 #!/usr/bin/env bash |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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2 |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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3 BASE_LINK="https://raw.githubusercontent.com/nunofonseca/fastq_utils/master/tests" |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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4 |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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5 BAR11_FILE="barcode_test_1.fastq.gz" |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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6 BAR12_FILE="barcode_test_2.fastq.gz" |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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7 BAR21_FILE="barcode_test2_1.fastq.gz" |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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8 BAR22_FILE="barcode_test2_2.fastq.gz" |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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9 INTER_FILE="inter.fastq.gz" |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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10 A1_FILE="a_1.fastq.gz" |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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11 POLYAT_FILE="poly_at.fastq.gz" |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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12 POLYAT3_FILE="poly_at_len3.fastq.gz" |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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13 TEST212_FILE="test_21_2.fastq.gz" |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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14 |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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15 BAR11_LINK=$BASE_LINK"/"$BAR11_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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16 BAR12_LINK=$BASE_LINK"/"$BAR12_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
diff
changeset
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17 BAR21_LINK=$BASE_LINK"/"$BAR21_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
diff
changeset
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18 BAR22_LINK=$BASE_LINK"/"$BAR22_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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19 INTER_LINK=$BASE_LINK"/"$INTER_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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changeset
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20 A1_LINK=$BASE_LINK"/"$A1_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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21 POLYAT_LINK=$BASE_LINK"/"$POLYAT_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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22 POLYAT3_LINK=$BASE_LINK"/"$POLYAT3_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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23 TEST212_LINK=$BASE_LINK"/"$TEST212_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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24 |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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25 function get_data { |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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26 local link=$1 |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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27 local fname=$2 |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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28 |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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29 if [ ! -f $fname ]; then |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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30 echo "$fname not available locally, downloading.." |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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31 wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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32 fi |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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33 } |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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34 |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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35 # Get test data |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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36 pushd test-data |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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37 |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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38 get_data $BAR11_LINK $BAR11_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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39 get_data $BAR12_LINK $BAR12_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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40 get_data $BAR21_LINK $BAR21_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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41 get_data $BAR22_LINK $BAR22_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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42 get_data $INTER_LINK $INTER_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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43 get_data $A1_LINK $A1_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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44 get_data $POLYAT_LINK $POLYAT_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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45 get_data $TEST212_LINK $TEST212_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
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46 get_data $POLYAT3_LINK $POLYAT3_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
parents:
diff
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47 get_data $TEST212_LINK $TEST212_FILE |
df87d29fac7f
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
ebi-gxa
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48 get_data $POLYAT3_LINK $POLYAT3_FILE |