A paper prepared by the Yale Law School for the Indonesian Human Rights Campaign in 2004 found:
The Indonesian military and
security forces have engaged in widespread violence and extrajudicial killings in West Papua.
It goes on saying:
They have subjected Papuan men and women to acts of torture, disappearance, rape, and sexual violence, thus causing serious bodily and mental harm.
It turns out this is a genocide, not just murder and rape:
the historical and contemporary evidence set out above strongly suggests that the Indonesian government has committed proscribed acts with the intent to destroy the West Papuans as such, in violation of the 1948 Convention on the Prevention and Punishment of the Crime of Genocide and the customary
international law prohibition this Convention embodies.
A video published in 2010 on YouTube Report from Channel 4 News in the UK shows:
horrific torture of West Papuan civilians by the Indonesian military.
Warning: Disturbing footage and scenes there.
A public report to the U.N. Commission on Human Rights in 1999, the Special Rapporteur on Violence Against Women concluded that the Indonesian security forces used rape in West Papua:
as an instrument of torture and intimidation
and:
torture of women detained by the Indonesian security forces was widespread.
The picture you see is referenced in http://freewestpapua.org/ as:

Apartheid in West Papua. Civilians are led away like slaves after being detained following a peaceful meeting. October 2011
Additionally:
UN General Assembly. (2006). Resolution adopted by the General Assembly on 15 March 2006.
60/251. Human Rights Council. Retrieved from http://daccess-ddsny.un.org/doc/UNDOC/GEN/N05/502/66/PDF/N0550266.pdf?OpenElement
Mr. Kalosil on the question of West Papua:
It is clear from many historical records that the Melanesian people of West Papua were the scapegoats of cold war politics and were sacrificed to gratify the appetite for natural resources which this country possesses.
How can we then ignore hundreds of thousands of West Papuans who have been brutally beaten and murdered? The people of West Papua are looking to the UN as a beacon for hope. It is time for the UN to move beyond its periphery and address and rectify some historical error.
Another reference:
Embassy of the Republic of Indonesia in London. (2009). Facts on Indonesia’s Sovereignty over Irian Jaya (Papua and West Papua Provinces). Retrieved from
www.indonesianembassy.org.uk/papua/papua.html
Summary: Since 1963's withdrawal of the Dutch colonial administration, the Free Papua Movement (OPM)
has conducted a low-level guerilla war against Indonesia, targeting its military and police, and
kidnapping non-Papuan Indonesian settlers and foreigners
More evidence:
Indonesia has signed the 1998 UN Convention against Torture yet members of the
Indonesian forces in West Papua continue to physically harm civilians in and outside of
prisons, such as the 300 people beaten or tortured following a pro-independence
Congress in October 2011.
Source: Franciscans International. (2012). Widespread incidence of torture in the provinces of Papua
and West Papua in Indonesia. Retrieved from http://daccess-ddsny.un.org/doc/UNDOC/GEN/G12/106/20/PDF/G1210620.pdf?OpenElement
Finally, a definitive final document:
GriffMUN2014
Briefing Paper for United Nations Human Rights Council
rights abuses by Indonesian forces in West Papua.
Flora Varitimos and Riley Kernaghan.
Documents almost all pieces of evidence showing that there has been a genocide against West Papua civilians. The document also argues that:
abuses reported as occurring in West Papua may be violations of
international law and to international treaties and conventions by which Indonesia is bound.