updating auspice with npm install --global auspice@2.29.1
This is the report
npm WARN deprecated linspace@1.0.0: I wrote this module a very long time ago; you should use something else.
npm WARN deprecated redux-devtools@3.7.0: Package moved to @redux-devtools/core.
npm WARN deprecated request@2.88.2: request has been deprecated, see Requestâs Past, Present and Future ¡ Issue #3142 ¡ request/request ¡ GitHub
npm WARN deprecated core-js@2.6.12: core-js@<3.3 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
npm WARN deprecated redux-devtools-instrument@1.10.0: Package moved to @redux-devtools/instrument.
npm WARN deprecated har-validator@5.1.5: this library is no longer supported
npm WARN deprecated uuid@3.4.0: Please upgrade to version 7 or higher. Older versions may use Math.random() in certain circumstances, which is known to be problematic. See Thereâs Math.random(), and then thereâs Math.random() ¡ V8 for details.
npm WARN deprecated urix@0.1.0: Please see GitHub - lydell/urix: [DEPRECATED] Makes Windows-style paths more unix and URI friendly.
npm WARN deprecated resolve-url@0.2.1: GitHub - lydell/resolve-url: [DEPRECATED] Like Node.jsâ `path.resolve`/`url.resolve` for the browser.
npm WARN deprecated querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
npm WARN deprecated chokidar@2.1.8: Chokidar 2 will break on node v14+. Upgrade to chokidar 3 with 15x less dependencies.
npm WARN deprecated fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@~2.3.2 (node_modules/auspice/node_modules/chokidar/node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@2.3.2: wanted {âosâ:âdarwinâ,âarchâ:âanyâ} (current: {âosâ:âlinuxâ,âarchâ:âx64â})
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@^1.2.7 (node_modules/auspice/node_modules/watchpack-chokidar2/node_modules/chokidar/node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@1.2.13: wanted {âosâ:âdarwinâ,âarchâ:âanyâ} (current: {âosâ:âlinuxâ,âarchâ:âx64â})
npm WARN react-addons-css-transition-group@15.6.2 requires a peer of react@^15.4.2 but none is installed. You must install peer dependencies yourself.
npm ERR! code EEXIST
npm ERR! syscall symlink
npm ERR! path âŚ/lib/node_modules/auspice/auspice.js
npm ERR! dest /home/kimberleyb/miniconda3/envs/nextstrain/bin/auspice
npm ERR! errno -17
npm ERR! EEXIST: file already exists, symlink ââŚ/lib/node_modules/auspice/auspice.jsâ â â/home/kimberleyb/miniconda3/envs/nextstrain/bin/auspiceâ
npm ERR! File exists: /home/kimberleyb/miniconda3/envs/nextstrain/bin/auspice
npm ERR! Remove the existing file and try again, or run npm
npm ERR! with --force to overwrite files recklessly.
npm ERR! A complete log of this run can be found in:
npm ERR! /home/kimberleyb/.npm/_logs/2021-07-26T11_53_10_321Z-debug.log
running auspice --version gives the following:
/home/kimberleyb/miniconda3/envs/nextstrain/bin/auspice: line 2: syntax error near unexpected token newline' /home/kimberleyb/miniconda3/envs/nextstrain/bin/auspice: line 2:
Usage: npm â
**augur update with **
conda install -c conda-forge -c bioconda augur=12
this is the report
Collecting package metadata (current_repodata.json): done
Solving environment: done
Package Plan
environment location: /home/kimberleyb/miniconda3/envs/nextstrain
added / updated specs:
- augur=12
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2021.7.5-h~ â conda-forge::ca-certificates-2021.5.30-ha878542_0
certifi pkgs/main::certifi-2021.5.30-py38h06a~ â conda-forge::certifi-2021.5.30-py38h578d9bd_0
openssl pkgs/main::openssl-1.1.1k-h27cfd23_0 â conda-forge::openssl-1.1.1k-h7f98852_0
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
running augur --version gives the following:
augur 12.0.0
so it seems that augur is ok now regarding the version, however I still get the same error with the config file colors.tsv where I indicated the field âyearâ with specified colors for each years. As indicated by emma, this was due to the augur version I was using. What was going wrong was the âvalidationâ step inside of âexportâ which checks that the resulting files make sense. But since that fails, Snakemake protects you from a âbad runâ by deleting the resulting files. I since then use a workaround suggested by emma.
auspice is not ok either.
btw adding the path to auspice view command helped.
Kim