即使文件保存在容器中，我也找不到输出文件

Question

我找不到使用Windows powershell的arpeggio输出文件（该算法是为Linux创建的）

我尝试添加>；创建输出文本文件，但这仅创建以下内容的输出文件：

INFO//08:56:42.365//Program begin.
INFO//08:56:42.402//Loaded PDB structure (BioPython)
INFO//08:56:42.403//Detected that the input structure contains hydrogens. Hydrogen addition will be skipped.
INFO//08:56:42.630//Loaded PDB structure (OpenBabel)
INFO//08:56:42.640//Mapped OB to BioPython atoms and vice-versa.
INFO//08:56:42.780//Typed atoms.
INFO//08:56:42.789//Determined atom explicit and implicit valences, bond orders, atomic numbers, formal charge and number of bound hydrogens.
INFO//08:56:42.826//Initialised SIFts.
WARNING//08:56:42.830//Chain termini could not be determined for chain E. It may not be a polypeptide chain.
INFO//08:56:42.831//Determined polypeptide residues, chain breaks, termini
INFO//08:56:43.009//Percieved and stored rings.
INFO//08:56:43.034//Perceived and stored amide groups.
INFO//08:56:43.039//Added hydrogens to BioPython atoms.
INFO//08:56:43.045//Added VdW radii.
INFO//08:56:43.050//Added covalent radii.
INFO//08:56:43.053//Completed NeighborSearch.
INFO//08:56:43.058//Assigned rings to residues.
INFO//08:56:43.061//Made selection.
INFO//08:56:43.173//Expanded to binding site.
INFO//08:56:43.174//Flagged selection rings.
INFO//08:56:43.175//Completed new NeighbourSearch.
INFO//08:56:43.245//Calculated pairwise contacts.
INFO//08:56:43.386//Program End. Maximum memory usage was 83.82 MB.

如您所见，文件是创建并保存在某个地方的，但是当我运行cat时，我找不到开发人员建议作为输出文件的任何文件

docker run --rm -v C:\directory:/<path to file> -it arpeggio python arpeggio.py /file -s RESNAME:xxx -v

在这之后，我应该能够运行python show_contacts.py file.pdb -s来显示PyMOL上的交互

PS Z:\> docker run arpeggio python show_contacts.py fie.pdb -s
But, this is the outcome
docker : Traceback (most recent call last):
At line:1 char:1
+ docker run arpeggio python show_contacts.py file.pdb -s
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : NotSpecified: (Traceback (most recent call last)::String) [], RemoteException
    + FullyQualifiedErrorId : NativeCommandError

  File "show_contacts.py", line 509, in <module>
    with open(contacts_filename, 'rb') as fo:
IOError: [Errno 2] No such file or directory: '/arpeggio/file.contacts'

因此，没有创建输出文件 知道为什么吗

Answer 1

我可以通过在PowerShell中运行以下代码来解决此问题：

docker run  rm -v :/<host-directory>:/<container-path> -u uid:gid -it arpeggio python arpeggio.py /container-path/file.pdb -s RESNAME:xxx -v

在运行Ubuntu18.04并将docker ce作为一个子系统拉到Windows上之后，我能够得到我的uid和gid，我必须澄清，如果在docker上添加-H localhost:2375并在右键单击docker并单击Settings之后选择“Expose daemon”，同样的代码在docker中也很有用

希望这对任何有同样问题的人都有用