Commit eb8124e4 authored by Bharath Ramsundar's avatar Bharath Ramsundar Committed by GitHub
Browse files

Merge pull request #344 from ktaneishi/issue341 

append '-c' option to wget commands.
parents 30036392 e902650a

deepchem/dock/docking.py

+2 −2
Original line number Diff line number Diff line
@@ -34,7 +34,7 @@ class VinaGridRFDocker(Docker): 
    """Builds model."""

    self.base_dir = tempfile.mkdtemp()

    print("About to download trained model.")

    call(("wget http://deepchem.io.s3-website-us-west-1.amazonaws.com/trained_models/random_full_RF.tar.gz").split())

    call(("wget -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/trained_models/random_full_RF.tar.gz").split())

    call(("tar -zxvf random_full_RF.tar.gz").split())

    call(("mv random_full_RF %s" % (self.base_dir)).split())

    self.model_dir = os.path.join(self.base_dir, "random_full_RF")
@@ -60,7 +60,7 @@ class VinaGridDNNDocker(object): 
    """Builds model."""

    self.base_dir = tempfile.mkdtemp()

    print("About to download trained model.")

    call(("wget http://deepchem.io.s3-website-us-west-1.amazonaws.com/trained_models/random_full_DNN.tar.gz").split())

    call(("wget -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/trained_models/random_full_DNN.tar.gz").split())

    call(("tar -zxvf random_full_DNN.tar.gz").split())

    call(("mv random_full_DNN %s" % (self.base_dir)).split())

    self.model_dir = os.path.join(self.base_dir, "random_full_DNN")

deepchem/dock/pose_generation.py

+1 −1
Original line number Diff line number Diff line
@@ -66,7 +66,7 @@ class VinaPoseGenerator(PoseGenerator): 
      print("Vina not available. Downloading")

      # TODO(rbharath): May want to move this file to S3 so we can ensure it's

      # always available.

      wget_cmd = "wget http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz"

      wget_cmd = "wget -c http://vina.scripps.edu/download/autodock_vina_1_1_2_linux_x86.tgz"

      call(wget_cmd.split())

      print("Downloaded Vina. Extracting")

      download_cmd = "tar xzvf autodock_vina_1_1_2_linux_x86.tgz"

deepchem/dock/tests/test_pose_scoring.py

+1 −1
Original line number Diff line number Diff line
@@ -25,7 +25,7 @@ class TestPoseScoring(unittest.TestCase): 
  """

  def setUp(self):

    """Downloads dataset."""

    call("wget http://deepchem.io.s3-website-us-west-1.amazonaws.com/featurized_datasets/core_grid.tar.gz".split())

    call("wget -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/featurized_datasets/core_grid.tar.gz".split())

    call("tar -zxvf core_grid.tar.gz".split())

    self.core_dataset = dc.data.DiskDataset("core_grid/")

examples/kaggle/get_kaggle.sh

+3 −3
Original line number Diff line number Diff line 
wget http://deepchem.io.s3-website-us-west-1.amazonaws.com/datasets/KAGGLE_training_disguised_combined_full.csv.gz

wget http://deepchem.io.s3-website-us-west-1.amazonaws.com/datasets/KAGGLE_test1_disguised_combined_full.csv.gz

wget http://deepchem.io.s3-website-us-west-1.amazonaws.com/datasets/KAGGLE_test2_disguised_combined_full.csv.gz
 
wget -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/datasets/KAGGLE_training_disguised_combined_full.csv.gz

wget -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/datasets/KAGGLE_test1_disguised_combined_full.csv.gz

wget -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/datasets/KAGGLE_test2_disguised_combined_full.csv.gz

examples/pdbbind/get_featurized_pdbbind.sh

+3 −3
Original line number Diff line number Diff line 
echo "Pulling featurized core pdbbind dataset from deepchem"

wget http://deepchem.io.s3-website-us-west-1.amazonaws.com/featurized_datasets/core_grid.tar.gz

wget -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/featurized_datasets/core_grid.tar.gz

echo "Extracting core pdbbind"

tar -zxvf core_grid.tar.gz

echo "Pulling featurized refined pdbbind dataset from deepchem"

wget http://deepchem.io.s3-website-us-west-1.amazonaws.com/featurized_datasets/refined_grid.tar.gz

wget -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/featurized_datasets/refined_grid.tar.gz

echo "Extracting refined pdbbind"

tar -zxvf refined_grid.tar.gz

echo "Pulling featurized full pdbbind dataset from deepchem"

wget http://deepchem.io.s3-website-us-west-1.amazonaws.com/featurized_datasets/full_grid.tar.gz

wget -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/featurized_datasets/full_grid.tar.gz

echo "Extracting full pdbbind"

tar -zxvf full_grid.tar.gz

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