Mercurial > repos > yhoogstrate > ega_download_streamer

annotate ega_download_streamer.xml @ 5:8af9d199e410 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 63cc1d3eba84a01ae7e9da734ed91f5b531e4a91-dirty
author yhoogstrate
date Tue, 29 Mar 2016 06:56:26 -0400
parents 887159f23385
children 4be485e48065
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1 <tool id="ega_download_streamer" name="EGA Download streamer" version="2.1.6.g0">
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2 <description>data from the European Genome-phenome Archive in a secure manner</description>
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3 <requirements>
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4 <requirement type="package" version="2.1.6">EGA_download_streamer</requirement>
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5 </requirements>
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6 <stdio>
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7 <!-- Anything other than zero is an error -->
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8 <regex match="Login failed" source="both" level="fatal"/>
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9 <regex match="error:" source="both" level="fatal"/>
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10 <exit_code range="1:" />
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11 <exit_code range=":-1" />
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12 </stdio>
2
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13 <version_command>java -jar $JAVA_JAR_PATH"/EgaDemoClient.jar" -version | grep -i Version | grep -v -i new</version_command>
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14 <command><![CDATA[
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15 #import random
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16 #import string
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18 #set $encryption_key = ''.join(random.SystemRandom().choice(string.ascii_uppercase + string.ascii_lowercase + string.digits) for _ in range(2048))
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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))
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21 echo \$user > credentials.txt &&
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22 echo \$pass >> credentials.txt &&
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24 echo "Creating an encryption request at server" &&
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25 java -jar
3
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26 "\$JAVA_JAR_PATH/EgaDemoClient.jar"
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27 -pf "credentials.txt"
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28 -rf "$ega_file_identifier"
a939b87382e0 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c
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29 -re "$encryption_key"
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30 -label "${random_request_uid}" | grep -v "Login failed" &&
a939b87382e0 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 72bbd9452fb48044cfafb0074b49a67a8530ff9c
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31
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32 echo "" &&
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33 echo "" &&
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34 echo "" &&
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35 echo "Downloading request" &&
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36 java -jar
3
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37 "\$JAVA_JAR_PATH/EgaDemoClient.jar"
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38 -pf "credentials.txt"
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39 -dr "${random_request_uid}"
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40 -nt 7 > download.log ;
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41
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42 cat download.log &&
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43
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44 ## Commands below may fail if authentication was not a success
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45 ENCRYPTED_FILES_NAME=\$(grep -oE "Completed Download Target:[ ]+(.*?)\.cip" download.log | sed -r "s/^Completed Download Target:[ ]+//" ) &&
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46 DECRYPTED_FILES_NAME=\${ENCRYPTED_FILES_NAME%.cip} &&
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47
4
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48 echo "" &&
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49 echo "" &&
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50 echo "" &&
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51 echo "Decrpyting \$ENCRYPTED_FILES_NAME to \$DECRYPTED_FILES_NAME" &&
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52 java -jar
3
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53 "\$JAVA_JAR_PATH/EgaDemoClient.jar"
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54 -pf credentials.txt
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55 -dc "\$ENCRYPTED_FILES_NAME"
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56 -dck "$encryption_key" &&
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57
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58 if file --mime-type "\$DECRYPTED_FILES_NAME" | grep -q /gzip$; then
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59 echo "Unpacking as well" &&
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60 gunzip -cf "\$DECRYPTED_FILES_NAME" > "$output" ;
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61 else
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62 mv "\$DECRYPTED_FILES_NAME" "$output" ;
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63 fi ;
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64
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65 echo "Cleaning up credentials" &&
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66 echo "overwriten" > "credentials.txt" &&
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67 rm "credentials.txt"
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68 ]]></command>
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69 <inputs>
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70 <param name="ega_file_identifier" type="text" value="" label="Identifier of the file in EGA" />
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71 </inputs>
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72 <outputs>
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73 <data name="output" auto_format="true" label="${tool.name} on ${ega_file_identifier}" />
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="ega_file_identifier" value="EGAF00001059069" />
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78
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79 <output name="output" file="EGAF00001059069.fastq" />
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80 </test>
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81 </tests>
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82
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83 <help>
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84 **What it does**
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85
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86 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 must be decrypted using the streamer after download is complete.
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87
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88 To download a given dataset, the user should provide the corresponding EGA file identifier (e.g. EGAF00001059069).
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90 **Configuration**
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91
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92 The admin has to configure the server such that the environment variables $user and $pass are exported and reflect the credentials of the EGA account. The user and password shall not be visible to users. This can also be done in the config/jobs_conf.xml file.
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94 https://www.ebi.ac.uk/ega/about/your_EGA_account/download_streaming_client
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95 </help>
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97 <citations>
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98 </citations>
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99 </tool>