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jmchilton/gist:00b6a9cad4a78207c5075d2f584838a7

Created September 27, 2016 19:59
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gistfile1.txt
$ mulled-build --recipes-dir ../bioconda-recipes --targets 'samtools=1.3.1,bedtools=2.22' build
./involucro -v=3 -f /home/john/workspace/galaxy-lib/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='bioconda,conda-forge,r' -set TEST='true' -set TARGETS='samtools=1.3.1,bedtools=2.22' -set REPO='quay.io/mulled/mulled-v1-a93fa17175d6f093a6423535399b7ad4ac06ceed' build
[Sep 27 15:58:40] DEBU Run file [/home/john/workspace/galaxy-lib/galaxy/tools/deps/mulled/invfile.lua]
[Sep 27 15:58:40] STEP Run image [continuumio/miniconda:latest] with command [[rm -rf /data/dist]]
[Sep 27 15:58:40] DEBU Creating container [step-4ff4f7eeac]
[Sep 27 15:58:40] DEBU Created container [eb5cdfab2b12 step-4ff4f7eeac], starting it
[Sep 27 15:58:40] DEBU Container [eb5cdfab2b12 step-4ff4f7eeac] started, waiting for completion
[Sep 27 15:58:40] DEBU Container [eb5cdfab2b12 step-4ff4f7eeac] completed with exit code [0] as expected
[Sep 27 15:58:40] DEBU Container [eb5cdfab2b12 step-4ff4f7eeac] removed
[Sep 27 15:58:40] STEP Run image [continuumio/miniconda:latest] with command [[/bin/sh -c conda install -c bioconda -c conda-forge -c r samtools=1.3.1 bedtools=2.22 -p /usr/local --copy --yes]]
[Sep 27 15:58:40] DEBU Creating container [step-4d17783052]
[Sep 27 15:58:41] DEBU Created container [e036bf15919b step-4d17783052], starting it
[Sep 27 15:58:41] DEBU Container [e036bf15919b step-4d17783052] started, waiting for completion
[Sep 27 15:58:49] SOUT Fetching package metadata: ..........
[Sep 27 15:58:49] SOUT Solving package specifications: .........
[Sep 27 15:58:51] SOUT
[Sep 27 15:58:51] SOUT Package plan for installation in environment /usr/local:
[Sep 27 15:58:51] SOUT
[Sep 27 15:58:51] SOUT The following packages will be downloaded:
[Sep 27 15:58:51] SOUT
[Sep 27 15:58:51] SOUT package | build
[Sep 27 15:58:51] SOUT ---------------------------|-----------------
[Sep 27 15:58:51] SOUT bedtools-2.22 | 0 731 KB
[Sep 27 15:58:51] SOUT ncurses-5.9 | 9 954 KB
[Sep 27 15:58:51] SOUT openssl-1.0.2j | 0 3.2 MB
[Sep 27 15:58:51] SOUT zlib-1.2.8 | 3 87 KB
[Sep 27 15:58:51] SOUT curl-7.49.1 | 1 542 KB
[Sep 27 15:58:51] SOUT samtools-1.3.1 | 3 1.4 MB
[Sep 27 15:58:51] SOUT ------------------------------------------------------------
[Sep 27 15:58:51] SOUT Total: 6.9 MB
[Sep 27 15:58:51] SOUT
[Sep 27 15:58:51] SOUT The following NEW packages will be INSTALLED:
[Sep 27 15:58:51] SOUT
[Sep 27 15:58:51] SOUT bedtools: 2.22-0 (copy)
[Sep 27 15:58:51] SOUT curl: 7.49.1-1 (copy)
[Sep 27 15:58:51] SOUT ncurses: 5.9-9 (copy)
[Sep 27 15:58:51] SOUT openssl: 1.0.2j-0 (copy)
[Sep 27 15:58:51] SOUT samtools: 1.3.1-3 (copy)
[Sep 27 15:58:51] SOUT zlib: 1.2.8-3 (copy)
[Sep 27 15:58:51] SOUT
[Sep 27 15:58:51] SOUT Fetching packages ...
bedtools-2.22- 100% |###############################| Time: 0:00:00 1.06 MB/s: --:--:-- 0.00 B/s
ncurses-5.9-9. 100% |###############################| Time: 0:00:00 1.41 MB/s: --:--:-- 0.00 B/s
openssl-1.0.2j 100% |###############################| Time: 0:00:01 2.35 MB/s: --:--:-- 0.00 B/s
zlib-1.2.8-3.t 100% |###############################| Time: 0:00:00 411.42 kB/s: --:--:-- 0.00 B/s
curl-7.49.1-1. 100% |###############################| Time: 0:00:00 973.95 kB/s: --:--:-- 0.00 B/s
samtools-1.3.1 100% |###############################| Time: 0:00:00 1.57 MB/s: --:--:-- 0.00 B/s
[Sep 27 15:59:02] SOUT Extracting packages ...
[ COMPLETE ]|##################################################| 100% | 0%
[Sep 27 15:59:02] SOUT Linking packages ...
[ COMPLETE ]|##################################################| 100% | 0%
[Sep 27 15:59:03] DEBU Container [e036bf15919b step-4d17783052] completed with exit code [0] as expected
[Sep 27 15:59:03] DEBU Container [e036bf15919b step-4d17783052] removed
[Sep 27 15:59:03] STEP Wrap [build/dist] as [quay.io/mulled/mulled-v1-a93fa17175d6f093a6423535399b7ad4ac06ceed]
[Sep 27 15:59:03] DEBU Creating container [step-97863e9673]
[Sep 27 15:59:03] DEBU Packing succeeded
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