Mercurial > repos > iuc > package_blast_plus_2_2_31
annotate tool_dependencies.xml @ 1:c0c4580bee85 draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 883c08829881671274c0a6ccb11046c6f5eadd9c
| author | peterjc |
|---|---|
| date | Thu, 24 Sep 2015 05:41:18 -0400 |
| parents | a2b8e3898680 |
| children | 4df9cdbc6e61 |
| rev | line source |
|---|---|
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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1 <?xml version='1.0' encoding='utf-8'?> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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2 <tool_dependency> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
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3 <package name="blast+" version="2.2.31"> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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4 <install version="1.0"> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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5 <actions_group> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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6 <!-- Download the binaries for BLAST+ compatible with 64-bit OSX. --> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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7 <actions os="darwin" architecture="x86_64"> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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8 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-universal-macosx.tar.gz</action> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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9 <action type="move_directory_files"> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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10 <source_directory>bin</source_directory> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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11 <destination_directory>$INSTALL_DIR</destination_directory> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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12 </action> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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13 </actions> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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14 <!-- Download the binaries for BLAST+ compatible with 32-bit OSX. --> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
diff
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15 <actions os="darwin" architecture="i386"> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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16 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-universal-macosx.tar.gz</action> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
diff
changeset
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17 <action type="move_directory_files"> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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18 <source_directory>bin</source_directory> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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19 <destination_directory>$INSTALL_DIR</destination_directory> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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20 </action> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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21 </actions> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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22 <!-- Download the binaries for BLAST+ compatible with 64-bit Linux. --> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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23 <actions os="linux" architecture="x86_64"> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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24 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-x64-linux.tar.gz</action> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
diff
changeset
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25 <action type="move_directory_files"> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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26 <source_directory>bin</source_directory> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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changeset
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27 <destination_directory>$INSTALL_DIR</destination_directory> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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28 </action> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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29 </actions> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
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30 <actions> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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31 <action type="shell_command">echo "ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported."</action> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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32 <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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33 <action type="shell_command">uname</action> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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34 <action type="shell_command">arch</action> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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35 <action type="shell_command">echo "Please report this via https://github.com/peterjc/galaxy_blast/issues - thank you!"</action> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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36 <action type="shell_command">false</action> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
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37 <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install --> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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38 </actions> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
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39 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. --> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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40 <action type="set_environment"> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
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41 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
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42 <environment_variable name="BLAST_ROOT_DIR" action="set_to">$INSTALL_DIR</environment_variable> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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43 </action> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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44 </actions_group> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
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45 </install> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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46 <readme> |
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1
c0c4580bee85
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 883c08829881671274c0a6ccb11046c6f5eadd9c
peterjc
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47 Downloads the precompiled 64 bit Linux, or Mac OS X BLAST+ binaries from the NCBI, |
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c0c4580bee85
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 883c08829881671274c0a6ccb11046c6f5eadd9c
peterjc
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48 which is faster than performing a local compliation, avoids any issues with build |
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c0c4580bee85
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 883c08829881671274c0a6ccb11046c6f5eadd9c
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49 dependencies, and is more reproducible between installations as there is no |
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c0c4580bee85
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 883c08829881671274c0a6ccb11046c6f5eadd9c
peterjc
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50 variability from the compiler or library versions. |
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c0c4580bee85
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 883c08829881671274c0a6ccb11046c6f5eadd9c
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51 |
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c0c4580bee85
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 883c08829881671274c0a6ccb11046c6f5eadd9c
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52 Note that as of BLAST+ 2.2.31 the NCBI do not provide 32 bit Linux binaries. |
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0
a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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53 |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
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54 For more details, see: |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
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55 http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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56 </readme> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
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57 </package> |
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a2b8e3898680
planemo upload for repository https://github.com/peterjc/galaxy_blast/packages/package_blast_plus_2_2_31 commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
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58 </tool_dependency> |