Mercurial > repos > yhoogstrate > ega_download_streamer

annotate ega_download_streamer.xml @ 5:3e2cccf08053 draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/ega_download_streamer commit 9a111d610dcc3ea6a10d6a21769bc8d15c2cd41d
author yhoogstrate
date Thu, 17 Nov 2016 05:40:55 -0500
parents 42fbce72bc07
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
yhoogstrate
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1 <tool id="ega_download_streamer" name="EGA Download streamer" version="2.1.6.g0">
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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2 <description>data from the European Genome-phenome Archive in a secure manner</description>
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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3 <requirements>
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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4 <requirement type="package" version="2.1.6">EGA_download_streamer</requirement>
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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5 </requirements>
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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6 <stdio>
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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7 <!-- Anything other than zero is an error -->
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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8 <regex match="Login failed" source="both" level="fatal"/>
1
5bfcb2bffd03 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit addbb78198534683454365526f6df5cdb7846bf6-dirty
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9 <regex match="error:" source="both" level="fatal"/>
0
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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10 <exit_code range="1:" />
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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11 <exit_code range=":-1" />
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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12 </stdio>
1
5bfcb2bffd03 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit addbb78198534683454365526f6df5cdb7846bf6-dirty
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13 <version_command>java -jar $JAVA_JAR_PATH"/EgaDemoClient.jar" -version | grep -i Version | grep -v -i new</version_command>
0
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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14 <command><![CDATA[
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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15 #import random
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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16 #import string
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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17
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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18 #set $encryption_key = ''.join(random.SystemRandom().choice(string.ascii_uppercase + string.ascii_lowercase + string.digits) for _ in range(2048))
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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19 #set $random_request_uid = 'request_'+str($ega_file_identifier)+'_'+''.join(random.SystemRandom().choice(string.ascii_uppercase + string.ascii_lowercase + string.digits) for _ in range(64))
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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20
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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21 echo \$user > credentials.txt &&
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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22 echo \$pass >> credentials.txt &&
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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23
3
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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24 echo "Creating an encryption request at server:" &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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25
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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26 if java -jar
2
4a8332665db3 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 63cc1d3eba84a01ae7e9da734ed91f5b531e4a91-dirty
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27 "\$JAVA_JAR_PATH/EgaDemoClient.jar"
0
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28 -pf "credentials.txt"
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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29 -rf "$ega_file_identifier"
0add1e8d751a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c-dirty
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30 -re "$encryption_key"
3
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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31 -label "${random_request_uid}" | grep -v "Login failed" > request.log ; then
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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32
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33 cat request.log &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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34 echo "" &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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35 echo "" &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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36 echo "" &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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37 echo "Downloading request:" &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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38
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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39 if java -jar
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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40 "\$JAVA_JAR_PATH/EgaDemoClient.jar"
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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41 -pf "credentials.txt"
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
yhoogstrate
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42 -dr "${random_request_uid}"
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
yhoogstrate
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43 -nt 7 > download.log ; then
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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44
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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45 cat download.log &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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46
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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47 ## Commands below may fail if authentication was not a success
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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48 ENCRYPTED_FILES_NAME=\$(grep -oE "Completed Download Target:[ ]+(.*?)\.cip" download.log | sed -r "s/^Completed Download Target:[ ]+//" ) &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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49 DECRYPTED_FILES_NAME=\${ENCRYPTED_FILES_NAME%.cip} &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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50
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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51 echo "" &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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52 echo "" &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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53 echo "" &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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54 echo "Decrpyting \$ENCRYPTED_FILES_NAME to \$DECRYPTED_FILES_NAME:" &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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55
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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56 if java -jar
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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57 "\$JAVA_JAR_PATH/EgaDemoClient.jar"
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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58 -pf credentials.txt
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59 -dc "\$ENCRYPTED_FILES_NAME"
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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60 -dck "$encryption_key" > decrypt.log ; then
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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61
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62 cat decrypt.log &&
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63
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64 if file --mime-type "\$DECRYPTED_FILES_NAME" | grep -q /gzip\$; then
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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65
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66 echo "" &&
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67 echo "" &&
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68 echo "" &&
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69 echo "Unpacking because it is an archive" &&
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70 gunzip -cf "\$DECRYPTED_FILES_NAME" > "$output" ;
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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71
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72 else
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73 mv "\$DECRYPTED_FILES_NAME" "$output" ;
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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74 fi ;
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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75
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76 else
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77 echo "Error: decrypting failed:" 1>&2 &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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78 cat decrypt.log &&
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79 exit 1 ;
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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80 fi ;
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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81
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82 else
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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83 echo "Error: downloading the request failed:" 1>&2 &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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84 cat download.log &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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85 exit 1 ;
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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86 fi ;
0
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87
3
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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88 else
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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89 echo "Error: making the request failed" 1>&2 &&
a1f6611f0533 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
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90 cat request.log &&
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91 exit 1 ;
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92 fi &&
0
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93
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94
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95 echo "Cleaning up credentials" &&
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96 echo "overwriten" > "credentials.txt" &&
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97 rm "credentials.txt"
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98 ]]></command>
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99 <inputs>
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100 <param name="ega_file_identifier" type="text" value="" label="Identifier of the file in EGA" />
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101 </inputs>
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102 <outputs>
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103 <data name="output" auto_format="true" label="${tool.name} on ${ega_file_identifier}" />
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104 </outputs>
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105 <tests>
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106 <test>
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107 <param name="ega_file_identifier" value="EGAF00001059069" />
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108
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109 <output name="output" file="EGAF00001059069.fastq" />
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110 </test>
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111 </tests>
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112
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113 <help>
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114 **What it does**
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115
4
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116 Individual files or whole datasets may be downloaded from European Genome-phenome Archive (EGA) in a secure manner by first placing a download request and then downloading the file/s associated with the request. All files are automatically encrypted prior to streaming and shall be decrypted using the streamer after downloading has completed.
0
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117
4
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118 **How to use**
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119
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120 When you load the tool in galaxy, the user should provide the corresponding EGA file identifier (e.g. EGAF00001059069).
0
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121
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122 **Configuration**
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123
4
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124 The admin has to configure a generic account, further described in the README: https://raw.githubusercontent.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper/master/README.rst
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125
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126 https://www.ebi.ac.uk/ega/about/your_EGA_account/download_streaming_client
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127 </help>
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128
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129 <citations>
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130 </citations>
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131 </tool>