I am new to Github and I want to upload some scripts that I developed during my research. One of the scripts requires the use of a small external program (not mine) whose source code is included as supplemental material in a journal paper. Can I upload the program and/or the source code of that program?
The journal is Computers & Geosciences.
The answer to your question depends entirely on the license of the "small external program (not yours)". Where did it come from? Find its source and read the terms of the license.
If it's an open source license or a free software license, usually you are permitted to redistribute it so long as you preserve attribution and license terms in the code header. If it's a different type of license, then it will depend entirely on the content of the license, which acts like a contract between the author and yourself.
UPDATE w/ JOURNAL SPECIFIC DETAILS:
The Journal of Computers & Geosciences is published by Elsevier who has an open access publishing option for authors. If the paper in question was published as open access, and its chosen license was CC-BY, then that gives you permission to reuse the work (including the attached source-code) so long as you provide attribution. If the article in question wasn't published as open access, then you'll have to contact the authors or locate another source for the code that has clear licensing terms.
Unless the source code comes with a licence that explicitly allows you what you want to do, you have to get the permission of the current copyright holders to be on the safe side. These may either be the authors of the article, the publisher or both – depending on what copyright transfer happened between the authors and the journal.
However, it is very likely that the authors are fine with you reusing their source code; this may be one of their intentions for publishing it. Authors that have a problem with this, usually do not publish their source code. As a reusing of the source code raises the chance of the paper being cited, the journal is likely to endorse what you want as well.
Thus it is unlikely that anybody sues you, but on the other hand, if you write a mail asking the authors and the journal for permission, you are likely to get a positive answer (and they may consider to equip their code with a permissive licence next time).
