Mercurial > repos > fubar > tool_factory_2
view getlocalrpackages.py @ 25:9fe74bd23af2 draft
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author | fubar |
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date | Mon, 02 Mar 2015 05:18:21 -0500 |
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import os import subprocess import sys def find_packages(prefix="package_r_"): """ """ #locate env.sh | grep -i package_r_ #/data/extended/galaxyJune14_2014/tool_dependency/readline/6.2/devteam/package_r_2_15_0/8ab0d08a3da1/env.sh #/data/home/rlazarus/galaxy/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/5f1b8d22140a/env.sh #/data/home/rlazarus/galaxy/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/d9964efbfbe3/env.sh #/data/home/rlazarus/galtest/tool_dependency_dir/R_3_1_1/3.1.1/fubar/package_r_3_1_1/63cdb9b2234c/env.sh eprefix = prefix if prefix.find('/') <> -1: eprefix = prefix.replace('/','\/') # for grep path = '.' # fails on nitesh's recent mac - locate not working # cl = ['locate env.sh | grep -i %s' % eprefix,] cl = ['find %s -iname "env.sh" | grep -i %s' % (path,eprefix),] p = subprocess.Popen(cl, stdout=subprocess.PIPE, stderr=subprocess.PIPE,shell=True) out, err = p.communicate() fpaths = out.split('\n') fpaths = [x for x in fpaths if len(x) > 1] fver = [x.split(os.path.sep)[-4:-1] for x in fpaths] # >>> foo.split(os.path.sep)[-4:-1] # ['fubar', 'package_r_3_1_1', '63cdb9b2234c'] if len(fpaths) > 0: res = [['%s rev %s owner %s' % (x[1],x[2],x[0]),fpaths[i],False] for i,x in enumerate(fver)] res.insert(0,['Use default (system) interpreter','system',False]) else: res = [['Use default (system) interpreter','system',False], ['**WARNING** NO package env.sh files found - is the "find" system command working? Are any interpreters installed?','system',True]] if len(res) > 2: res[1][2] = True # selected if more than one # return a triplet - user_sees,value,selected - all unselected if False return res def testapi(): host_url = 'http://localhost:8080' new_path = [ os.path.join( os.getcwd(), "lib" ) ] new_path.extend( sys.path[1:] ) # remove scripts/ from the path sys.path = new_path from galaxy import config aconfig = config.Configuration( ) M_A_K = aconfig.master_api_key tooldeps = aconfig.tool_dependency_dir gi = GalaxyInstance(url=host_url, key=M_A_K) if __name__ == "__main__": print find_packages()