commit/galaxy-central: greg: Code cleanup for uploading files to a repo in the tool shed.
1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e0de7ec40a80/ changeset: e0de7ec40a80 branches: user: greg date: 2011-06-06 21:45:16 summary: Code cleanup for uploading files to a repo in the tool shed. affected #: 3 files (8.8 KB) --- a/lib/galaxy/webapps/community/controllers/repository.py Mon Jun 06 15:30:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Mon Jun 06 15:45:16 2011 -0400 @@ -16,9 +16,12 @@ # Characters that must be html escaped MAPPED_CHARS = { '>' :'>', - '<' :'<' } + '<' :'<', + '"' : '"', + '&' : '&', + '\'' : ''' } MAX_CONTENT_SIZE = 32768 -VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;" ) +VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) class CategoryListGrid( grids.Grid ): @@ -673,7 +676,7 @@ for i, line in enumerate( open( file_path ) ): to_html = '%s%s' % ( to_html, self.to_html_str( line ) ) if len( to_html ) > MAX_CONTENT_SIZE: - large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %d\n' % MAX_CONTENT_SIZE + large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE ) to_html = '%s%s' % ( to_html, self.to_html_str( large_str ) ) break return to_html @@ -706,9 +709,9 @@ translated.append( ' ' ) elif c == '\t': translated.append( ' ' ) - elif c in [ '\r\n', '\n' ]: + elif c == '\n': translated.append( '<br/>' ) - else: + elif c not in [ '\r' ]: translated.append( 'X' ) return ''.join( translated ) def __build_allow_push_select_field( self, trans, current_push_list, selected_value='none' ): --- a/lib/galaxy/webapps/community/controllers/upload.py Mon Jun 06 15:30:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Mon Jun 06 15:45:16 2011 -0400 @@ -60,12 +60,9 @@ elif file_data not in ( '', None ): uploaded_file = file_data.file if uploaded_file: - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we update without passing the -r null flag (see below). When - # we're uploading more files, we have to clean out the repo root directory - # so we can move them into it. We need to eliminate all this when we figure - # out how to browse the repository files. + # Our current support for browsing repo contents requires a copy of the + # repository files in the repo root directory. To produce these copies, + # we update without passing the "-r null" flag. os.chdir( repo_dir ) os.system( 'hg update -r null > /dev/null 2>&1' ) os.chdir( current_working_dir ) @@ -76,16 +73,16 @@ tar = tarfile.open( uploaded_file.name ) istar = True except tarfile.ReadError, e: + tar = None istar = False - if istar: - ok, message = self.__check_archive( tar ) - if ok: - if repository.is_new: + if repository.is_new: + if istar: + # We have an archive ( a tarball ) + ok, message = self.__check_archive( tar ) + if ok: tar.extractall( path=repo_dir ) tar.close() uploaded_file.close() - # TODO: The following will only work on new, empty repos, - # need to also handle repos with existing contents for root, dirs, files in os.walk( repo_dir, topdown=False ): # Don't visit .hg directories and don't include hgrc files in commit. if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: @@ -109,78 +106,9 @@ repo.dirstate.add( file_path ) files_to_commit.append( file_path ) else: - # The repo already contains the file, so we need to make sure the file being - # uploaded is different from the file in the repo. This is a temporary brute- - # force method. - # Make a clone of the repository in a temporary location - tmp_dir = tempfile.mkdtemp() - tmp_archive_dir = os.path.join( tmp_dir, 'tmp_archive_dir' ) - if not os.path.exists( tmp_archive_dir ): - os.makedirs( tmp_archive_dir ) - cmd = "hg clone %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) - os.chdir( tmp_archive_dir ) - os.system( cmd ) - os.chdir( current_working_dir ) - cloned_repo_dir = os.path.join( tmp_archive_dir, 'repo_%d' % repository.id ) - if upload_point is not None: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, file_data.filename ) ) - else: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, file_data.filename ) ) - # Extract the uploaded tarball to the load_point within the cloned repository hierarchy - tar.extractall( path=full_path ) tar.close() - uploaded_file.close() - # We want these change sets to be associated with the owner of the repository, so we'll - # set the HGUSER environment variable accordingly. - os.environ[ 'HGUSER' ] = trans.user.username - # Add the file to the cloned repository. If it's already tracked, this should do nothing. - os.chdir( cloned_repo_dir ) - os.system( 'hg add > /dev/null 2>&1' ) - os.chdir( current_working_dir ) - os.chdir( cloned_repo_dir ) - # Commit the change set to the cloned repository - os.system( "hg commit -m '%s' > /dev/null 2>&1" % commit_message ) - os.chdir( current_working_dir ) - # Push the change set to the master repository - cmd = "hg push %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) - os.chdir( cloned_repo_dir ) - os.system( cmd ) - # Change the current working directory to the original - os.chdir( current_working_dir ) - # Since we extracted the archive into repo_dir, a copy of the archive's - # files remains there. The following will remove them. It would be - # more ideal if we could use the mercurial api to do this, but I haven't - # yet discovered a way to pass the -r null flag to repo.update(). - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we'll update without passing the -r null flag. When we figure - # out how to browse the repository files, uncomment the -r flag below. - os.chdir( repo_dir ) - os.system( 'hg update > /dev/null 2>&1' ) - os.chdir( current_working_dir ) - # Remove tmp directory - shutil.rmtree( tmp_dir ) - message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename - trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repository', - message=message, - id=trans.security.encode_id( repository.id ) ) ) - - else: - tar.close() - else: - """ - # TODO: This segment uses the mercurial api (and works), but we need the - # api section below to be functional in order for this segment to be used. - # In the meantime, we use the repository.is_new check below... - repo_contains = file_path in [ i for i in ctx.manifest() ] - if not repo_contains: - repo.dirstate.add( file_path ) - files_to_commit.append( file_path ) - """ - if repository.is_new: - # We're uploading a single file + # We have a single file if upload_point is not None: full_path = os.path.abspath( os.path.join( upload_point, file_data.filename ) ) file_path = os.path.join( upload_point, file_data.filename ) @@ -190,98 +118,18 @@ shutil.move( uploaded_file.name, full_path ) repo.dirstate.add( file_path ) files_to_commit.append( file_path ) - else: - """ - # TODO: This segment attempts to use the mercurial api, but is not functional. - # Until we get it working, we're using the brute force method below it. - fctx = None - for changeset in repo.changelog: - ctx = repo.changectx( changeset ) - if file_path not in ctx.files(): - continue - fctx = ctx[ file_path ] - break - # We now have the parent version of the upload file. - if fctx: - data = fctx.data() - # TODO: obviously very bad way of comparing files... - file_path_data = open( full_path ).read() - different = data != file_path_data - if different: - # TODO: how do you insert a new version of an existing file using the mercurial api??? - # the follwoin gis not correct! - #repo.dirstate.normallookup( file_path ) - #files_to_commit.append( file_path ) - pass - """ - # The repo already contains the file, so we need to make sure the file being - # uploaded is different from the file in the repo. This is a temporary brute- - # force method. - # Make a clone of the repository in a temporary location - tmp_dir = tempfile.mkdtemp() - tmp_archive_dir = os.path.join( tmp_dir, 'tmp_archive_dir' ) - if not os.path.exists( tmp_archive_dir ): - os.makedirs( tmp_archive_dir ) - cmd = "hg clone %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) - os.chdir( tmp_archive_dir ) - os.system( cmd ) - os.chdir( current_working_dir ) - cloned_repo_dir = os.path.join( tmp_archive_dir, 'repo_%d' % repository.id ) - if upload_point is not None: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, file_data.filename ) ) - else: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, file_data.filename ) ) - # Move the uploaded file to the load_point within the cloned repository hierarchy - shutil.move( uploaded_file.name, full_path ) - # We want these change sets to be associated with the owner of the repository, so we'll - # set the HGUSER environment variable accordingly. - os.environ[ 'HGUSER' ] = trans.user.username - # Add the file to the cloned repository. If it's already tracked, this should do nothing. - os.chdir( cloned_repo_dir ) - os.system( 'hg add > /dev/null 2>&1' ) - os.chdir( current_working_dir ) - os.chdir( cloned_repo_dir ) - # Commit the change set to the cloned repository - os.system( "hg commit -m '%s' > /dev/null 2>&1" % commit_message ) - os.chdir( current_working_dir ) - # Push the change set to the master repository - cmd = "hg push %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) - os.chdir( cloned_repo_dir ) - os.system( cmd ) - os.chdir( current_working_dir ) - # Since we extracted the archive into repo_dir, a copy of the archive's - # files remains there. The following will remove them. It would be - # more ideal if we could use the mercurial api to do this, but I haven't - # yet discovered a way to pass the -r null flag to repo.update(). - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we'll update without passing the -r null flag. When we figure - # out how to browse the repository files, uncomment the -r flag below. - os.chdir( repo_dir ) - os.system( 'hg update > /dev/null 2>&1' ) - os.chdir( current_working_dir ) - # Remove tmp directory - shutil.rmtree( tmp_dir ) - message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename - trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repository', - message=message, - id=trans.security.encode_id( repository.id ) ) ) + else: + # We're uploading files to a repository with existing + # contents, so clone the repository to a temporary location. + tmp_dir, cloned_repo_dir = self.__handle_hg_clone( trans, repository, upload_point, uploaded_file, file_data, repo_dir, current_working_dir, istar, tar=tar ) + # Commit and push the changes from the cloned repo to the master repo. + self.__handle_hg_push( trans, repository, file_data, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ) if ok: if files_to_commit: repo.dirstate.write() repo.commit( text=commit_message ) - # Since we extracted the archive into repo_dir, a copy of the archive's - # files remains there. The following will remove them. It would be - # more ideal if we could use the mercurial api to do this, but I haven't - # yet discovered a way to pass the -r null flag to repo.update(). - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we'll update without passing the -r null flag. When we figure - # out how to browse the repository files, uncomment the -r flag below. os.chdir( repo_dir ) os.system( 'hg update > /dev/null 2>&1' ) - #os.system( 'hg update -r null' ) os.chdir( current_working_dir ) message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename trans.response.send_redirect( web.url_for( controller='repository', @@ -290,17 +138,8 @@ id=trans.security.encode_id( repository.id ) ) ) else: status = 'error' - # Since we extracted the archive into repo_dir, a copy of the archive's - # files remains there. The following will remove them. It would be - # more ideal if we could use the mercurial api to do this, but I haven't - # yet discovered a way to pass the -r null flag to repo.update(). - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we'll update without passing the -r null flag. When we figure - # out how to browse the repository files, uncomment the -r flag below. os.chdir( repo_dir ) os.system( 'hg update > /dev/null 2>&1' ) - #os.system( 'hg update -r null' ) os.chdir( current_working_dir ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/community/repository/upload.mako', @@ -308,6 +147,57 @@ commit_message=commit_message, message=message, status=status ) + def __handle_hg_clone( self, trans, repository, upload_point, uploaded_file, file_data, repo_dir, current_working_dir, istar, tar=None ): + tmp_dir = tempfile.mkdtemp() + tmp_archive_dir = os.path.join( tmp_dir, 'tmp_archive_dir' ) + if not os.path.exists( tmp_archive_dir ): + os.makedirs( tmp_archive_dir ) + # Make a clone of the repository in a temporary location + cmd = "hg clone %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) + os.chdir( tmp_archive_dir ) + os.system( cmd ) + os.chdir( current_working_dir ) + cloned_repo_dir = os.path.join( tmp_archive_dir, 'repo_%d' % repository.id ) + if upload_point is not None: + full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, file_data.filename ) ) + else: + full_path = os.path.abspath( os.path.join( cloned_repo_dir, file_data.filename ) ) + if istar: + # Extract the uploaded tarball to the load_point within the cloned repository hierarchy + tar.extractall( path=full_path ) + tar.close() + uploaded_file.close() + else: + # Move the uploaded file to the load_point within the cloned repository hierarchy + shutil.move( uploaded_file.name, full_path ) + return tmp_dir, cloned_repo_dir + def __handle_hg_push( self, trans, repository, file_data, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ): + # We want these change sets to be associated with the owner of the repository, so we'll + # set the HGUSER environment variable accordingly. + os.environ[ 'HGUSER' ] = trans.user.username + # Add the file to the cloned repository. If it's already tracked, this should do nothing. + os.chdir( cloned_repo_dir ) + os.system( 'hg add > /dev/null 2>&1' ) + os.chdir( current_working_dir ) + os.chdir( cloned_repo_dir ) + # Commit the change set to the cloned repository + os.system( "hg commit -m '%s' > /dev/null 2>&1" % commit_message ) + os.chdir( current_working_dir ) + # Push the change set to the master repository + cmd = "hg push %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) + os.chdir( cloned_repo_dir ) + os.system( cmd ) + os.chdir( current_working_dir ) + # Make a copy of the updated repository files for browsing. + os.chdir( repo_dir ) + os.system( 'hg update > /dev/null 2>&1' ) + os.chdir( current_working_dir ) + shutil.rmtree( tmp_dir ) + message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename + trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repository', + message=message, + id=trans.security.encode_id( repository.id ) ) ) def __check_archive( self, archive ): for member in archive.getmembers(): # Allow regular files and directories only --- a/templates/webapps/community/upload/upload.mako Mon Jun 06 15:30:02 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,242 +0,0 @@ -<%namespace file="/message.mako" import="render_msg" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/community/base_panels.mako' - else: - return '/base.mako' -%> - -<%inherit file="${inherit(context)}"/> - -<% - if selected_upload_type == 'tool': - title = 'Upload a tool archive' - type_label = 'tool' - elif selected_upload_type == 'toolsuite': - title = 'Upload a tool suite archive' - type_label = 'tool suite' -%> - -<%def name="title()"> - ${title} -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - $( "#upload_form" ).submit(); - }); - }); - </script> -</%def> - -<h2>${title}</h2> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">${title}</div> - <div class="toolFormBody"> - ## TODO: nginx - <form id="upload_form" name="upload_form" action="${h.url_for( controller='tool_upload', action='upload' )}" enctype="multipart/form-data" method="post"> - %if replace_id is not None: - <input type='hidden' name="replace_id" value="${replace_id}"/> - %endif - <div class="form-row"> - <label>Upload Type</label> - <div class="form-row-input"> - ${upload_type_select_list.get_html()} - </div> - <div class="toolParamHelp" style="clear: both;"> - Need help creating a ${type_label} archive? See details below. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>File:</label> - <div class="form-row-input"><input type="file" name="file_data"/></div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Category</label> - <div class="form-row-input"> - <select name="category_id" multiple> - %for category in categories: - %if category.id in selected_categories: - <option value="${trans.security.encode_id( category.id )}" selected>${category.name}</option> - %else: - <option value="${trans.security.encode_id( category.id )}">${category.name}</option> - %endif - %endfor - </select> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>URL:</label> - <div class="form-row-input"><input type="text" name="url" style="width: 100%;"/></div> - <div class="toolParamHelp" style="clear: both;"> - Instead of uploading directly from your computer, you may instruct Galaxy to download the file from a Web or FTP address. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" class="primary-button" name="upload_button" value="Upload"> - </div> - </form> - </div> -</div> -<p/> -<div class="toolFormTitle">Creating an archive containing a tool or a suite of tools</div> -<p> - A tool or tool suite archive is a tar-format file (bzipped or gzipped tar are valid) - containing all the files necessary to load the tool(s) into a Galaxy instance. -</p> -%if selected_upload_type == 'toolsuite': - <h3>Tool Suite Archive</h3> - <p> - A tools suite must include a file named <code>suite_config.xml</code> which provides information about the id, name, - version and description of the tool suite, as well as the id, name, version and description of each tool - in the suite. Here is an example <code>suite_config.xml</code> file. - </p> - <p> -<pre> - <suite id="lastz_toolsuite" name="Suite of Lastz tools" version="1.0.0"> - <description>This suite contains all of my Lastz tools for Galaxy</description> - <tool id="lastz_wrapper_2" name="Lastz" version="1.1.0"> - <description> map short reads against reference sequence</description> - </tool> - <tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.0.0"> - <description> map short paired reads against reference sequence</description> - </tool> - </suite> -</pre> - </p> - </p> - <p> - New versions of the suite can be uploaded, replacing an older version of the suite, but the version attribute - of the <suite> tag must be altered the same way that the version attribute of a single tool config must be altered - if uploading a new version of a tool. - </p> - <p> - The id, name and version attributes of each <tool> tag in the <code>suite_config.xml</code> file must exactly match the same - attributes in each associated tool config in the archive or you will not be allowed to upload the archive. - </p> - <p> - In addition to the <code>suite_config.xml</code> file, the archive must include all - <a href="http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax" target="_blank">tool config files</a>, - executables, functional test data (if your tool config includes functional tests) and other files needed for each - of the tools in your suite to function within Galaxy. See the information about single tool archives below for - additional hints to enable ease-of-use when others download your suite of tools. - </p> - <p> - For example, to package the above Lastz suite of tools: -<pre> - user@host:~% tar jcvf ~/Desktop/galaxy_lastz_toolsuite.tar.bz2 lastzsuite - lastzsuite/ - lastzsuite/README - lastzsuite/suite_config.xml - lastzsuite/lastz_paired_reads_wrapper.py - lastzsuite/lastz_paired_reads_wrapper.xml - lastzsuite/lastz_wrapper.py - lastzsuite/lastz_wrapper.xml - lastzsuite/lastz-distrib-1.02.00/ - lastzsuite/lastz-distrib-1.02.00/src/ - lastzsuite/lastz-distrib-1.02.00/src/Makefile - lastzsuite/lastz-distrib-1.02.00/src/version.mak - lastzsuite/lastz-distrib-1.02.00/src/lastz.c - lastzsuite/lastz-distrib-1.02.00/src/lastz.h - ... -</pre> - ~/Desktop/galaxy_lastz_tool.tar.bz2 is now ready to be uploaded. - </p> -%endif -<h3>Single Tool Archive</h3> -<p> - A single tool archive must include a - <a href="http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax" target="_blank">tool config file</a> - and will probably also include a tool script. If any steps are necessary to install your tool beyond the basic - instructions below, include a README file to provide details. If the tool (or parts of it) are written in C, - the source code can be included (or put links to the source in the README). Do not include pre-compiled binaries - without source since Galaxy is run on a wide variety of platforms. Also, if you are only wrapping or providing a - Galaxy config for a tool that is not your own, be sure the license allows for redistribution before including any - part of that tool in the archive. -</p> -<p> - There are no requirements about the directory structure inside the archive, but for ease of use it's generally - a good idea to put everything inside a sub-directory, instead of directly at the top level. -</p> -<p> - For example, to package the Lastz tool's config file, Galaxy wrapper, and the C source: -<pre> - user@host:~% tar jcvf ~/Desktop/galaxy_lastz_tool.tar.bz2 lastz - lastz/ - lastz/README - lastz/lastz_wrapper.py - lastz/lastz_wrapper.xml - lastz/lastz-distrib-1.02.00/ - lastz/lastz-distrib-1.02.00/src/ - lastz/lastz-distrib-1.02.00/src/Makefile - lastz/lastz-distrib-1.02.00/src/version.mak - lastz/lastz-distrib-1.02.00/src/lastz.c - lastz/lastz-distrib-1.02.00/src/lastz.h - ... -</pre> - ~/Desktop/galaxy_lastz_tool.tar.bz2 is now ready to be uploaded. -</p> -<h3>Editing Information, Categories, and Submitting For Approval</h3> -<p> - Simply uploading a tool to the Galaxy too shed will not allow other users to find and download your tool. It will - need to be approved by an administrator before it appears in the tool list. -</p> -<p> - After your archive has successfully uploaded, you will be redirected to the Edit Tool page. Provide a detailed - description of what the tool does - this will be used by administrators to understand the tool before approving it - for display on the site. Once approved, this information will be displayed to users who view your tool. In addition, - the site administrators will have configured a number of categories with which you can associate your tool to make it - easy to find by users looking to solve specific problems. Associate as many categories as are relevant to your tool. - You may change the description and associated categories as often as you'd like until you click the "<strong>Submit for - approval</strong>" button. Once submitted, the tool will be approved or rejected by an administrator. If the tool is - rejected, you will see information about why it was rejected, and you can make appropriate changes to the archive and - re-submit it for approval. When it is approved, your archive will be visible to everyone. At that point, the description - and associated categories can only be changed by an administrator. -</p> -<p> - When the tool has been approved or rejected, you may upload a new version by browsing to the tool's "View Tool" page, - clicking the "Tool actions" menu in the upper right corner of the page, and selecting "Upload a new version" from the - menu. -</p> -<hr/> -<h3>Downloading and Installing Tools</h3> -<p> - A tool's download link will send you the tool archive. Once downloaded, unpack the tool on your local Galaxy instance's server: -<pre> - user@host:~% tar xvf galaxy_lastz_tool.tar - ... - user@host:~% tar zxvf galaxy_lastz_tool.tar.gz - ... - user@host:~% tar jxvf galaxy_lastz_tool.tar.bz2 - ... -</pre> - If the archive includes a README file, consult it for installation instructions. If not, follow these basic steps: - <ol> - <li>Create a directory under <code>galaxy_dist/tools/</code> to house downloaded tool(s).</li> - <li>In the new directory, place the XML and any script file(s) which were contained in the archive.</li> - <li> - If the tool includes binaries, you'll need to copy them to a directory on your <code>$PATH</code>. If the tool depends on - C binaries but does not come with them (only source), you'll need to compile the source first. - </li> - <li>Add the tool to <code>galaxy_dist/tool_conf.xml</code>.</li> - <li>Restart your Galaxy server process.</li> - </ol> -</p> -<p> - In the near future, we plan to implement a more direct method to install tools via the Galaxy administrator user interface instead - of placing files on the filesystem and manually managing the <code>tool_conf.xml</code> file. -</p> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.
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