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AlexsLemonade / OpenPBTA-manuscript

The manuscript repository for the Open Pediatric Brain Tumor Atlas Project
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Methods: telomerase activity prediction #76

Closed jaclyn-taroni closed 4 years ago

jaclyn-taroni commented 4 years ago

@NNoureen and @syzheng used their method EXTEND to quantify telomerase activity and performed a number of comparisons AlexsLemonade/OpenPBTA-analysis/analyses/telomerase-activity-prediction. This issue is to track the addition of a telomerase activity prediction section to the methods section of the manuscript.

NNoureen commented 4 years ago

Thanks. We have a problem. While building the build.sh we are getting some errors due to some analysis file links. Following is the error log. Kindly help us to resolve this issue.

(manubot) noureen@cbbi16:~/OpenPBTA-manuscript$ sh build/build.sh Retrieving and processing reference metadata

INFO

Manuscript content parts: 00.front-matter 01.abstract 02.introduction 03.methods 04.results 05.conclusions 90.back-matter

INFO

65 unique citations strings extracted from text 65 unique standard citations

INFO

requests-cache starting with 0 cached responses

WARNING

Error parsing web_query output as JSON for https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/analyses/immune-deconv/plots/corrplot_xCell_vs_CIBERSORT: Remote page not found

WARNING

Error in get_url_citeproc_zotero for https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/analyses/immune-deconv/plots/corrplot_xCell_vs_CIBERSORT due to a JSONDecodeError: Expecting value: line 1 column 1 (char 0)

INFO

Expecting value: line 1 column 1 (char 0) Traceback (most recent call last): File "/home/UTHSCSA/noureen/miniconda3/envs/manubot/lib/python3.6/site-packages/manubot/cite/url.py", line 17, in get_url_citeproc return retriever(url) File "/home/UTHSCSA/noureen/miniconda3/envs/manubot/lib/python3.6/site-packages/manubot/cite/url.py", line 35, in get_url_citeproc_zotero zotero_data = web_query(url) File "/home/UTHSCSA/noureen/miniconda3/envs/manubot/lib/python3.6/site-packages/manubot/cite/zotero.py", line 38, in web_query raise error File "/home/UTHSCSA/noureen/miniconda3/envs/manubot/lib/python3.6/site-packages/manubot/cite/zotero.py", line 35, in web_query zotero_data = response.json() File "/home/UTHSCSA/noureen/miniconda3/envs/manubot/lib/python3.6/site-packages/requests/models.py", line 897, in json return complexjson.loads(self.text, **kwargs) File "/home/UTHSCSA/noureen/miniconda3/envs/manubot/lib/python3.6/json/init.py", line 354, in loads return _default_decoder.decode(s) File "/home/UTHSCSA/noureen/miniconda3/envs/manubot/lib/python3.6/json/decoder.py", line 339, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/home/UTHSCSA/noureen/miniconda3/envs/manubot/lib/python3.6/json/decoder.py", line 357, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

WARNING

jaclyn-taroni commented 4 years ago

Tagging @cgreene as he has more Manubot experience. I have not built the manuscript locally myself.

jashapiro commented 4 years ago

Hi @NNoureen! Do you need to build locally for your updates? It may be fine to only update the content/03.methods.md file at this point with your methods, submit those changes as a pull request, and then let the automatic build on github take care of the rest.

NNoureen commented 4 years ago

Sure we will update the content/03.methods.md and will submit that. Thanks for the help.

jaclyn-taroni commented 4 years ago

Closed via #100