Mercurial > repos > fubar > tool_factory_2
comparison toolfactory/rgToolFactory2.py @ 107:18e616939a91 draft
Uploaded
| author | fubar |
|---|---|
| date | Sat, 28 Nov 2020 02:52:24 +0000 |
| parents | 6de08f44e551 |
| children | e878bfc6b80c |
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| 106:6de08f44e551 | 107:18e616939a91 |
|---|---|
| 723 def prun(container, tout, cl, user="biodocker"): | 723 def prun(container, tout, cl, user="biodocker"): |
| 724 rlog = container.exec_run(cl, user=user) | 724 rlog = container.exec_run(cl, user=user) |
| 725 slogl = str(rlog).split("\\n") | 725 slogl = str(rlog).split("\\n") |
| 726 slog = "\n".join(slogl) | 726 slog = "\n".join(slogl) |
| 727 tout.write(f"## got rlog {slog} from {cl}\n") | 727 tout.write(f"## got rlog {slog} from {cl}\n") |
| 728 | |
| 729 dgroup = grp.getgrnam("docker")[2] | |
| 730 if os.path.exists(self.tlog): | 728 if os.path.exists(self.tlog): |
| 731 tout = open(self.tlog, "a") | 729 tout = open(self.tlog, "a") |
| 732 else: | 730 else: |
| 733 tout = open(self.tlog, "w") | 731 tout = open(self.tlog, "w") |
| 734 planemoimage = "quay.io/fubar2/planemo-biocontainer" | 732 planemoimage = "quay.io/fubar2/planemo-biocontainer" |
| 747 "sleep 30m", | 745 "sleep 30m", |
| 748 detach=True, | 746 detach=True, |
| 749 user="biodocker", | 747 user="biodocker", |
| 750 volumes={f"{tvolname}": {"bind": "/toolfactory", "mode": "rw"}}, | 748 volumes={f"{tvolname}": {"bind": "/toolfactory", "mode": "rw"}}, |
| 751 ) | 749 ) |
| 752 cl = f"groupmod -g {dgroup} docker" | |
| 753 prun(container, tout, cl, user="root") | |
| 754 cl = f"mkdir -p {destdir}" | 750 cl = f"mkdir -p {destdir}" |
| 755 prun(container, tout, cl, user="root") | 751 prun(container, tout, cl, user="root") |
| 756 cl = f"rm -rf {destdir}/*" | 752 cl = f"rm -rf {destdir}/*" |
| 757 prun(container, tout, cl, user="root") | 753 prun(container, tout, cl, user="root") |
| 758 ptestpath = os.path.join(destdir, "tfout", xreal) | 754 ptestpath = os.path.join(destdir, "tfout", xreal) |
| 759 self.copy_to_container(self.tooloutdir, destdir, container) | 755 self.copy_to_container(self.tooloutdir, destdir, container) |
| 760 cl = "chmod -R a+rwx /toolfactory" | 756 cl = "chown -R biodocker /toolfactory" |
| 761 prun(container, tout, cl, user="root") | 757 prun(container, tout, cl, user="root") |
| 762 rlog = container.exec_run(f"ls -la {destdir}") | 758 rlog = container.exec_run(f"ls -la {destdir}") |
| 763 ptestcl = f"planemo test --update_test_data --no_cleanup --test_data {destdir}/tfout/test-data --galaxy_root /home/biodocker/galaxy-central {ptestpath}" | 759 ptestcl = f"planemo test --update_test_data --no_cleanup --test_data {destdir}/tfout/test-data --galaxy_root /home/biodocker/galaxy-central {ptestpath}" |
| 764 try: | 760 try: |
| 765 rlog = container.exec_run(ptestcl) | 761 rlog = container.exec_run(ptestcl) |