SET METADATA FOR MULTIPLE FILES UPON UPLOAD
Adding metadata to files just got easier. You can now import tabular metadata formats to the CGC and extract and assign metadata based on your manifest file. Learn more about this feature on our Knowledge Center.
IMPROVED ACCESS TO CCLE DATA ON THE CGC
We recently made data from Cancer Cell Line Encyclopedia (CCLE) available on the CGC via the CCLE public project. CCLE contains 1,285 open access BAM files produced by RNA-Sequencing, Whole Genome Sequencing, and Whole Exome Sequencing analyses on cancer cell lines. Now, you can browse CCLE and TCGA datasets through the Data Overview. We’ve also enabled searching for and accessing specific files in CCLE and TCGA via the Data Browser. Then, you can query that dataset by metadata, search by ID, and save or access queries. For instance, by choosing the CCLE dataset, you can now copy BAM files, try our workflows, and perform analyses right away.
WE’VE UPGRADED OUR TLS
As part of our efforts to enhance our security, we’ve recently upgraded our servers to use TLSv1 as the minimum cryptographic protocol. This may cause some older implementation of SSL/TLS like openssl v0.9.x to fail. Some default python installations (notably the default installation on Mac OSX) link to the older version of openssl libraries and try to negotiate an SSL connection that can prompt the following error when Python program tries to connect to our API:
[SSL: SSLV3_ALERT_HANDSHAKE_FAILURE] sslv3 alert handshake failure (_ssl.c:590)
If you are getting SSL handshake errors, check the output of the following command:
python -c "import ssl; print(ssl.OPENSSL_VERSION)" OpenSSL 0.9.8zh 14 Jan 2016
If your OpenSSL version is lower than 1.0.2, we recommend switching to a different Python distribution, such as Miniconda, which have new openssl libraries linked.
This issue could also be fixed by first installing newer versions of Python and OpenSSL with Homebrew. Then, reinstall the pyopenssl package by providing paths to the newer openssl libraries. You can do this with the following commands:
$ brew install python $ brew install openssl $ sudo env ARCHFLAGS="-arch x86_64" LDFLAGS="-L/usr/local/opt/openssl/lib" CFLAGS="-I/usr/local/opt/openssl/include" pip install --upgrade --force-reinstall PyOpenSSL