text: user1075: I have installed some ucsc tools on my Mac computer and it worked fine:
  Installation
  conda create --name ucsc-netchainsubset377 --channel bioconda --yes ucsc-netchainsubset=377
  
  Conda environment activation
  source activate ucsc-netchainsubset377
  
  Checking the tool's help
      netchainsubset
  netChainSubset - Create chain file with subset of chains that appear in the net
  usage:
     netChainSubset in.net in.chain out.chain
  options:
     -gapOut=gap.tab - Output gap sizes to file
     -type=XXX - Restrict output to particular type in net file
     -splitOnInsert - Split chain when get an insertion of another chain
     -wholeChains - Write entire chain references by net, don't split
      when a high-level net is encoundered.  This is useful when nets
      have been filtered.
     -skipMissing - skip chains that are not found instead of generating
      an error.  Useful if chains have been filtered.
  
  The same commands on GNU/Linux produced the following error:
  netchainsubset
  netchainsubset: command not found
  
  even though the tool seems to be installed successfully:
  Downloading and Extracting Packages
  ucsc-netchainsubset- | 310 KB    | ############################################################################ | 100%
  mysql-connector-c-6. | 4.4 MB    | ############################################################################ | 100%
  Preparing transaction: done
  Verifying transaction: done
  Executing transaction: done
  
  The same happened with ucsc-fatotwobit and ucsc-liftup and I would not be surprised if this behaviour affected the whole suite of ucsc programmes installed through conda.
  Anyone can suggest a solution?
  Update 5 minutes after posting
  Thanks to terdon, I printed the PATH when the conda environment was active and listed what was in the folder where conda installed the UCSC tool. 
  ls /mnt/home2/miska/cr517/anaconda3/envs/ucsc-netchainsubset377/bin
  c_rehash         libpng-config      mysql_config    openssl  pngfix
  libpng16-config  my_print_defaults  netChainSubset  perror   png-fix-itxt
  
  Then I typed netChainSubset and got the help page, suggesting the tool is installed and working. Interestingly, on Mac, the tool is also called netChainSubset but it seems it can be called with netchainsubsetor NETCHAINSUBset for that matter. The case doesn't seem to matter on mac. To make my code more portable, I am going to follow the case in the bin of where the tool is installed.
  Cheers terdon.
  Cheers.
  
  user1075: Short answer: respect the case of the tool name
  Longer story below
  Thanks to terdon, I printed the PATH when the conda environment was active and listed what was in the folder where conda installed the UCSC tool.
  ls /mnt/home2/miska/cr517/anaconda3/envs/ucsc-netchainsubset377/bin
  c_rehash         libpng-config      mysql_config    openssl  pngfix
  libpng16-config  my_print_defaults  netChainSubset  perror   png-fix-itxt
  Then I typed netChainSubset and got the help page, suggesting the tool is installed and working. Interestingly, on Mac, the tool is also called netChainSubset but it seems it can be called with netchainsubsetor NETCHAINSUBset for that matter. The case doesn't seem to matter on mac. To make my code more portable, I am going to follow the case in the bin of where the tool is installed.
  
original_text: 1075: <p>I have installed some ucsc tools on my Mac computer and it worked fine:</p>
  
  <h3>Installation</h3>
  
  <pre><code>conda create --name ucsc-netchainsubset377 --channel bioconda --yes ucsc-netchainsubset=377
  </code></pre>
  
  <h3>Conda environment activation</h3>
  
  <pre><code>source activate ucsc-netchainsubset377
  </code></pre>
  
  <h3>Checking the tool's help</h3>
  
  <pre><code>    netchainsubset
  netChainSubset - Create chain file with subset of chains that appear in the net
  usage:
     netChainSubset in.net in.chain out.chain
  options:
     -gapOut=gap.tab - Output gap sizes to file
     -type=XXX - Restrict output to particular type in net file
     -splitOnInsert - Split chain when get an insertion of another chain
     -wholeChains - Write entire chain references by net, don't split
      when a high-level net is encoundered.  This is useful when nets
      have been filtered.
     -skipMissing - skip chains that are not found instead of generating
      an error.  Useful if chains have been filtered.
  </code></pre>
  
  <p>The same commands on GNU/Linux produced the following error:</p>
  
  <pre><code>netchainsubset
  netchainsubset: command not found
  </code></pre>
  
  <p>even though the tool seems to be installed successfully:</p>
  
  <pre><code>Downloading and Extracting Packages
  ucsc-netchainsubset- | 310 KB    | ############################################################################ | 100%
  mysql-connector-c-6. | 4.4 MB    | ############################################################################ | 100%
  Preparing transaction: done
  Verifying transaction: done
  Executing transaction: done
  </code></pre>
  
  <p>The same happened with <code>ucsc-fatotwobit</code> and <code>ucsc-liftup</code> and I would not be surprised if this behaviour affected the whole suite of ucsc programmes installed through conda.</p>
  
  <p>Anyone can suggest a solution?</p>
  
  <h3>Update 5 minutes after posting</h3>
  
  <p>Thanks to terdon, I printed the PATH when the conda environment was active and listed what was in the folder where conda installed the UCSC tool. </p>
  
  <pre><code>ls /mnt/home2/miska/cr517/anaconda3/envs/ucsc-netchainsubset377/bin
  c_rehash         libpng-config      mysql_config    openssl  pngfix
  libpng16-config  my_print_defaults  netChainSubset  perror   png-fix-itxt
  </code></pre>
  
  <p>Then I typed <code>netChainSubset</code> and got the help page, suggesting the tool is installed and working. Interestingly, on Mac, the tool is also called <code>netChainSubset</code> but it seems it can be called with <code>netchainsubset</code>or <code>NETCHAINSUBset</code> for that matter. The case doesn't seem to matter on mac. To make my code more portable, I am going to follow the case in the <code>bin</code> of where the tool is installed.</p>
  
  <p>Cheers terdon.</p>
  
  <p>Cheers.</p>
   1075: <h2>Short answer: respect the case of the tool name</h2>
  
  <h2>Longer story below</h2>
  
  <p>Thanks to terdon, I printed the PATH when the conda environment was active and listed what was in the folder where conda installed the UCSC tool.</p>
  
  <p>ls /mnt/home2/miska/cr517/anaconda3/envs/ucsc-netchainsubset377/bin
  c_rehash         libpng-config      mysql_config    openssl  pngfix
  libpng16-config  my_print_defaults  netChainSubset  perror   png-fix-itxt</p>
  
  <p>Then I typed netChainSubset and got the help page, suggesting the tool is installed and working. Interestingly, on Mac, the tool is also called netChainSubset but it seems it can be called with netchainsubsetor NETCHAINSUBset for that matter. The case doesn't seem to matter on mac. To make my code more portable, I am going to follow the case in the bin of where the tool is installed.</p>
  